Ben Bolstad
| Snapshot Date: 2026-05-08 13:45 -0400 (Fri, 08 May 2026) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: devel |
| git_last_commit: 2d99771 |
| git_last_commit_date: 2026-04-28 08:32:08 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-09 15:11 -0400 (Sat, 09 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4890 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 259/2374 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BIOCCHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.77.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | ERRORS | | ||||||||
| See other builds for BufferedMatrix in R Universe. | |||||||||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.77.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BufferedMatrix_1.77.0.tar.gz |
| StartedAt: 2026-05-08 21:52:50 -0400 (Fri, 08 May 2026) |
| EndedAt: 2026-05-08 21:53:14 -0400 (Fri, 08 May 2026) |
| EllapsedTime: 24.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings BufferedMatrix_1.77.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-09 01:52:50 UTC
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.77.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BufferedMatrix’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup?
209 | $x^{power}$ elementwise of the matrix
| ^
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘Rcodetesting.R’
Running ‘c_code_level_tests.R’
Running ‘objectTesting.R’
Running ‘rawCalltesting.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.77.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function ‘dbm_ReadOnlyMode’:
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: ‘sort_double’ defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init_package.c -o init_package.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.24-bioc/R/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -L/home/biocbuild/bbs-3.24-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.24-bioc/R/site-library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘rowSums’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colSums’ in package ‘BufferedMatrix’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘BufferedMatrix’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘BufferedMatrix’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix", "BufferedMatrix", .libPaths());.C("dbm_c_tester",integer(1))
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
Adding Additional Column
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000
Reassigning values
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 3
Buffer Cols: 3
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Activating Row Buffer
In row mode: 1
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Squaring Last Column
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
5.000000 10.000000 15.000000 20.000000 25.000000 900.000000
Square rooting Last Row, then turing off Row Buffer
In row mode: 0
Checking on value that should be not be in column buffer2.236068
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
2.236068 3.162278 3.872983 4.472136 5.000000 30.000000
Single Indexing. Assign each value its square
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Resizing Buffers Smaller
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Activating Row Mode.
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
Activating ReadOnly Mode.
The results of assignment is: 0
Printing matrix reversed.
900.000000 625.000000 400.000000 225.000000 100.000000 25.000000
841.000000 576.000000 361.000000 196.000000 81.000000 16.000000
784.000000 529.000000 324.000000 169.000000 64.000000 9.000000
729.000000 484.000000 289.000000 144.000000 49.000000 -30.000000
676.000000 441.000000 256.000000 121.000000 -20.000000 -10.000000
[[1]]
[1] 0
>
> proc.time()
user system elapsed
0.246 0.039 0.272
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 480233 25.7 1053308 56.3 637571 34.1
Vcells 887253 6.8 8388608 64.0 2083896 15.9
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Fri May 8 21:53:05 2026"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Fri May 8 21:53:05 2026"
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
>
>
> RowMode(tmp2)
<pointer: 0x5c96b4647520>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Fri May 8 21:53:05 2026"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Fri May 8 21:53:05 2026"
>
> ColMode(tmp2)
<pointer: 0x5c96b4647520>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.3215614 0.8220234 0.04966470 -0.1853398
[2,] 0.9157669 -0.6548107 -0.06884171 -0.8085489
[3,] 0.1763804 -0.2204784 0.36670048 -0.1505062
[4,] 0.7233769 -1.0514484 -1.19458136 2.1126644
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.3215614 0.8220234 0.04966470 0.1853398
[2,] 0.9157669 0.6548107 0.06884171 0.8085489
[3,] 0.1763804 0.2204784 0.36670048 0.1505062
[4,] 0.7233769 1.0514484 1.19458136 2.1126644
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.0160652 0.9066551 0.2228558 0.4305111
[2,] 0.9569571 0.8092037 0.2623770 0.8991935
[3,] 0.4199766 0.4695513 0.6055580 0.3879513
[4,] 0.8505156 1.0254016 1.0929691 1.4535007
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 225.48221 34.88857 27.27822 29.49045
[2,] 35.48534 33.74685 27.69261 34.80048
[3,] 29.37615 29.91599 31.42228 29.03002
[4,] 34.22853 36.30546 37.12427 41.64767
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x5c96b54328f0>
> exp(tmp5)
<pointer: 0x5c96b54328f0>
> log(tmp5,2)
<pointer: 0x5c96b54328f0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 469.3117
> Min(tmp5)
[1] 52.91672
> mean(tmp5)
[1] 71.81762
> Sum(tmp5)
[1] 14363.52
> Var(tmp5)
[1] 864.6173
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 90.47958 70.75030 67.19250 71.12310 70.07226 70.42343 69.05126 66.89823
[9] 70.87553 71.30999
> rowSums(tmp5)
[1] 1809.592 1415.006 1343.850 1422.462 1401.445 1408.469 1381.025 1337.965
[9] 1417.511 1426.200
> rowVars(tmp5)
[1] 8071.30401 76.08687 53.12614 55.08330 72.03447 93.62235
[7] 46.23002 31.26110 79.30208 46.86741
> rowSd(tmp5)
[1] 89.840436 8.722779 7.288768 7.421812 8.487312 9.675864 6.799266
[8] 5.591163 8.905172 6.845978
> rowMax(tmp5)
[1] 469.31168 85.77935 83.28911 86.68417 87.06476 92.98963 82.12845
[8] 77.21652 88.72242 84.88749
> rowMin(tmp5)
[1] 56.77605 57.47349 55.96097 55.40768 57.15100 52.91672 58.00339 57.18830
[9] 55.06347 61.87567
>
> colMeans(tmp5)
[1] 107.42925 70.06018 67.96701 67.85846 66.28125 70.78239 70.66772
[8] 74.48567 70.03689 69.21587 67.97222 70.30606 70.42534 70.70516
[15] 69.93343 73.59775 64.23826 70.21179 69.71194 74.46574
> colSums(tmp5)
[1] 1074.2925 700.6018 679.6701 678.5846 662.8125 707.8239 706.6772
[8] 744.8567 700.3689 692.1587 679.7222 703.0606 704.2534 707.0516
[15] 699.3343 735.9775 642.3826 702.1179 697.1194 744.6574
> colVars(tmp5)
[1] 16187.53425 39.52999 89.97112 113.36738 89.60460 66.95455
[7] 57.38628 74.49246 18.21074 54.19560 74.91419 109.54106
[13] 181.35177 69.70097 58.03039 55.44070 20.06962 71.67236
[19] 25.45518 48.75738
> colSd(tmp5)
[1] 127.230241 6.287288 9.485311 10.647412 9.465971 8.182576
[7] 7.575373 8.630902 4.267405 7.361766 8.655298 10.466186
[13] 13.466691 8.348711 7.617768 7.445851 4.479913 8.465953
[19] 5.045313 6.982648
> colMax(tmp5)
[1] 469.31168 76.44400 81.45748 86.68417 82.12845 82.85400 81.66363
[8] 88.72242 76.41505 78.21416 86.29438 92.98963 95.19383 84.13447
[15] 82.68907 83.28911 70.65797 85.86812 80.17364 86.13429
> colMin(tmp5)
[1] 61.14260 61.65104 56.77605 57.04346 52.91672 59.40706 58.62017 63.49084
[9] 62.78105 58.89951 55.06347 57.47349 58.00339 59.70832 57.15100 61.59233
[17] 55.40768 57.79697 64.17336 62.36187
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 90.47958 70.75030 67.19250 71.12310 NA 70.42343 69.05126 66.89823
[9] 70.87553 71.30999
> rowSums(tmp5)
[1] 1809.592 1415.006 1343.850 1422.462 NA 1408.469 1381.025 1337.965
[9] 1417.511 1426.200
> rowVars(tmp5)
[1] 8071.30401 76.08687 53.12614 55.08330 71.45860 93.62235
[7] 46.23002 31.26110 79.30208 46.86741
> rowSd(tmp5)
[1] 89.840436 8.722779 7.288768 7.421812 8.453319 9.675864 6.799266
[8] 5.591163 8.905172 6.845978
> rowMax(tmp5)
[1] 469.31168 85.77935 83.28911 86.68417 NA 92.98963 82.12845
[8] 77.21652 88.72242 84.88749
> rowMin(tmp5)
[1] 56.77605 57.47349 55.96097 55.40768 NA 52.91672 58.00339 57.18830
[9] 55.06347 61.87567
>
> colMeans(tmp5)
[1] 107.42925 70.06018 67.96701 67.85846 66.28125 NA 70.66772
[8] 74.48567 70.03689 69.21587 67.97222 70.30606 70.42534 70.70516
[15] 69.93343 73.59775 64.23826 70.21179 69.71194 74.46574
> colSums(tmp5)
[1] 1074.2925 700.6018 679.6701 678.5846 662.8125 NA 706.6772
[8] 744.8567 700.3689 692.1587 679.7222 703.0606 704.2534 707.0516
[15] 699.3343 735.9775 642.3826 702.1179 697.1194 744.6574
> colVars(tmp5)
[1] 16187.53425 39.52999 89.97112 113.36738 89.60460 NA
[7] 57.38628 74.49246 18.21074 54.19560 74.91419 109.54106
[13] 181.35177 69.70097 58.03039 55.44070 20.06962 71.67236
[19] 25.45518 48.75738
> colSd(tmp5)
[1] 127.230241 6.287288 9.485311 10.647412 9.465971 NA
[7] 7.575373 8.630902 4.267405 7.361766 8.655298 10.466186
[13] 13.466691 8.348711 7.617768 7.445851 4.479913 8.465953
[19] 5.045313 6.982648
> colMax(tmp5)
[1] 469.31168 76.44400 81.45748 86.68417 82.12845 NA 81.66363
[8] 88.72242 76.41505 78.21416 86.29438 92.98963 95.19383 84.13447
[15] 82.68907 83.28911 70.65797 85.86812 80.17364 86.13429
> colMin(tmp5)
[1] 61.14260 61.65104 56.77605 57.04346 52.91672 NA 58.62017 63.49084
[9] 62.78105 58.89951 55.06347 57.47349 58.00339 59.70832 57.15100 61.59233
[17] 55.40768 57.79697 64.17336 62.36187
>
> Max(tmp5,na.rm=TRUE)
[1] 469.3117
> Min(tmp5,na.rm=TRUE)
[1] 52.91672
> mean(tmp5,na.rm=TRUE)
[1] 71.78193
> Sum(tmp5,na.rm=TRUE)
[1] 14284.6
> Var(tmp5,na.rm=TRUE)
[1] 868.728
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.47958 70.75030 67.19250 71.12310 69.60660 70.42343 69.05126 66.89823
[9] 70.87553 71.30999
> rowSums(tmp5,na.rm=TRUE)
[1] 1809.592 1415.006 1343.850 1422.462 1322.525 1408.469 1381.025 1337.965
[9] 1417.511 1426.200
> rowVars(tmp5,na.rm=TRUE)
[1] 8071.30401 76.08687 53.12614 55.08330 71.45860 93.62235
[7] 46.23002 31.26110 79.30208 46.86741
> rowSd(tmp5,na.rm=TRUE)
[1] 89.840436 8.722779 7.288768 7.421812 8.453319 9.675864 6.799266
[8] 5.591163 8.905172 6.845978
> rowMax(tmp5,na.rm=TRUE)
[1] 469.31168 85.77935 83.28911 86.68417 87.06476 92.98963 82.12845
[8] 77.21652 88.72242 84.88749
> rowMin(tmp5,na.rm=TRUE)
[1] 56.77605 57.47349 55.96097 55.40768 57.15100 52.91672 58.00339 57.18830
[9] 55.06347 61.87567
>
> colMeans(tmp5,na.rm=TRUE)
[1] 107.42925 70.06018 67.96701 67.85846 66.28125 69.87822 70.66772
[8] 74.48567 70.03689 69.21587 67.97222 70.30606 70.42534 70.70516
[15] 69.93343 73.59775 64.23826 70.21179 69.71194 74.46574
> colSums(tmp5,na.rm=TRUE)
[1] 1074.2925 700.6018 679.6701 678.5846 662.8125 628.9040 706.6772
[8] 744.8567 700.3689 692.1587 679.7222 703.0606 704.2534 707.0516
[15] 699.3343 735.9775 642.3826 702.1179 697.1194 744.6574
> colVars(tmp5,na.rm=TRUE)
[1] 16187.53425 39.52999 89.97112 113.36738 89.60460 66.12685
[7] 57.38628 74.49246 18.21074 54.19560 74.91419 109.54106
[13] 181.35177 69.70097 58.03039 55.44070 20.06962 71.67236
[19] 25.45518 48.75738
> colSd(tmp5,na.rm=TRUE)
[1] 127.230241 6.287288 9.485311 10.647412 9.465971 8.131842
[7] 7.575373 8.630902 4.267405 7.361766 8.655298 10.466186
[13] 13.466691 8.348711 7.617768 7.445851 4.479913 8.465953
[19] 5.045313 6.982648
> colMax(tmp5,na.rm=TRUE)
[1] 469.31168 76.44400 81.45748 86.68417 82.12845 82.85400 81.66363
[8] 88.72242 76.41505 78.21416 86.29438 92.98963 95.19383 84.13447
[15] 82.68907 83.28911 70.65797 85.86812 80.17364 86.13429
> colMin(tmp5,na.rm=TRUE)
[1] 61.14260 61.65104 56.77605 57.04346 52.91672 59.40706 58.62017 63.49084
[9] 62.78105 58.89951 55.06347 57.47349 58.00339 59.70832 57.15100 61.59233
[17] 55.40768 57.79697 64.17336 62.36187
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.47958 70.75030 67.19250 71.12310 NaN 70.42343 69.05126 66.89823
[9] 70.87553 71.30999
> rowSums(tmp5,na.rm=TRUE)
[1] 1809.592 1415.006 1343.850 1422.462 0.000 1408.469 1381.025 1337.965
[9] 1417.511 1426.200
> rowVars(tmp5,na.rm=TRUE)
[1] 8071.30401 76.08687 53.12614 55.08330 NA 93.62235
[7] 46.23002 31.26110 79.30208 46.86741
> rowSd(tmp5,na.rm=TRUE)
[1] 89.840436 8.722779 7.288768 7.421812 NA 9.675864 6.799266
[8] 5.591163 8.905172 6.845978
> rowMax(tmp5,na.rm=TRUE)
[1] 469.31168 85.77935 83.28911 86.68417 NA 92.98963 82.12845
[8] 77.21652 88.72242 84.88749
> rowMin(tmp5,na.rm=TRUE)
[1] 56.77605 57.47349 55.96097 55.40768 NA 52.91672 58.00339 57.18830
[9] 55.06347 61.87567
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 111.95227 69.36425 68.90509 68.34999 66.84334 NaN 71.02923
[8] 73.87164 70.18000 68.21606 68.07763 69.37382 68.57652 71.44699
[15] 71.35370 74.93168 64.08327 69.63941 70.32734 73.83048
> colSums(tmp5,na.rm=TRUE)
[1] 1007.5704 624.2782 620.1458 615.1499 601.5900 0.0000 639.2631
[8] 664.8448 631.6200 613.9446 612.6987 624.3644 617.1886 643.0229
[15] 642.1833 674.3851 576.7494 626.7547 632.9460 664.4743
> colVars(tmp5,na.rm=TRUE)
[1] 17980.82717 39.02256 91.31755 124.82029 97.25081 NA
[7] 63.08926 79.56241 20.25667 49.72433 84.15345 113.45669
[13] 165.56652 72.22257 42.59106 42.35271 22.30807 76.94574
[19] 24.37654 50.31203
> colSd(tmp5,na.rm=TRUE)
[1] 134.092607 6.246804 9.556022 11.172300 9.861582 NA
[7] 7.942875 8.919777 4.500741 7.051548 9.173519 10.651605
[13] 12.867265 8.498386 6.526183 6.507896 4.723142 8.771872
[19] 4.937260 7.093097
> colMax(tmp5,na.rm=TRUE)
[1] 469.31168 76.44400 81.45748 86.68417 82.12845 -Inf 81.66363
[8] 88.72242 76.41505 77.12586 86.29438 92.98963 95.19383 84.13447
[15] 82.68907 83.28911 70.65797 85.86812 80.17364 86.13429
> colMin(tmp5,na.rm=TRUE)
[1] 61.14260 61.65104 56.77605 57.04346 52.91672 Inf 58.62017 63.49084
[9] 62.78105 58.89951 55.06347 57.47349 58.00339 59.70832 62.33112 66.37427
[17] 55.40768 57.79697 64.31375 62.36187
>
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 3
> which.col <- 1
> cat(which.row," ",which.col,"\n")
3 1
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> rowVars(tmp5,na.rm=TRUE)
[1] 441.84683 415.42486 177.47564 186.71324 414.79441 240.92336 198.12310
[8] 72.25563 115.46247 186.94250
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 441.84683 415.42486 177.47564 186.71324 414.79441 240.92336 198.12310
[8] 72.25563 115.46247 186.94250
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] -1.136868e-13 5.684342e-14 -2.842171e-14 -1.136868e-13 2.842171e-14
[6] -5.684342e-14 1.136868e-13 5.684342e-14 1.421085e-13 0.000000e+00
[11] -1.989520e-13 2.842171e-14 -8.526513e-14 5.684342e-14 -5.684342e-14
[16] 0.000000e+00 -5.684342e-14 5.684342e-14 1.136868e-13 3.552714e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
8 6
9 16
10 16
7 2
1 11
5 15
3 11
8 2
2 1
1 4
1 13
1 19
1 20
8 7
2 11
6 14
2 10
7 11
7 6
4 13
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 3.447499
> Min(tmp)
[1] -2.135993
> mean(tmp)
[1] -0.1161473
> Sum(tmp)
[1] -11.61473
> Var(tmp)
[1] 1.108369
>
> rowMeans(tmp)
[1] -0.1161473
> rowSums(tmp)
[1] -11.61473
> rowVars(tmp)
[1] 1.108369
> rowSd(tmp)
[1] 1.052791
> rowMax(tmp)
[1] 3.447499
> rowMin(tmp)
[1] -2.135993
>
> colMeans(tmp)
[1] -1.43005392 -1.06254889 -1.33908377 0.67412609 0.86042477 0.20530428
[7] -0.12613618 0.18232360 -0.59158429 -1.37738792 -0.47667344 0.21062821
[13] -1.07970948 -0.76752848 -1.02612292 -0.85402295 -0.37255026 -0.70144278
[19] -0.45570336 -1.32050719 -0.48455264 0.98794220 2.13578438 0.35351042
[25] 0.78857958 0.06953550 -1.16836335 -0.80259072 3.44749872 -0.73836080
[31] 0.60483082 0.75043598 2.41863291 -0.72627038 0.08194523 -0.30694708
[37] -0.53175787 0.70691792 -0.28716086 -0.14643420 0.45323509 2.19516040
[43] -0.74101643 -1.36870443 -0.39506221 -0.05122619 -1.62330585 0.84494821
[49] 0.60220952 -0.68531037 1.44626354 1.18244260 -1.99020087 -2.13599301
[55] -0.33312725 0.23014343 -0.30548586 -0.62826055 0.63085981 -1.07926364
[61] -0.17234820 0.82628398 -0.64334720 0.87199185 1.45010879 -0.11656597
[67] 0.23611047 -0.40289121 1.02185662 0.44080198 -0.98394440 -0.35536935
[73] -1.04860402 0.47313115 -1.98012096 0.40833997 -0.73087657 0.87533633
[79] -0.06745004 -0.51703977 0.82916982 1.94841476 -1.07821685 0.20579781
[85] -1.13496423 -0.12237210 -1.25933684 0.81421018 -0.39754751 -1.12308516
[91] -0.95328410 1.91065282 0.31874195 -1.99279247 -1.50632767 0.72551098
[97] -1.95772320 0.85986552 -0.51347947 0.67339457
> colSums(tmp)
[1] -1.43005392 -1.06254889 -1.33908377 0.67412609 0.86042477 0.20530428
[7] -0.12613618 0.18232360 -0.59158429 -1.37738792 -0.47667344 0.21062821
[13] -1.07970948 -0.76752848 -1.02612292 -0.85402295 -0.37255026 -0.70144278
[19] -0.45570336 -1.32050719 -0.48455264 0.98794220 2.13578438 0.35351042
[25] 0.78857958 0.06953550 -1.16836335 -0.80259072 3.44749872 -0.73836080
[31] 0.60483082 0.75043598 2.41863291 -0.72627038 0.08194523 -0.30694708
[37] -0.53175787 0.70691792 -0.28716086 -0.14643420 0.45323509 2.19516040
[43] -0.74101643 -1.36870443 -0.39506221 -0.05122619 -1.62330585 0.84494821
[49] 0.60220952 -0.68531037 1.44626354 1.18244260 -1.99020087 -2.13599301
[55] -0.33312725 0.23014343 -0.30548586 -0.62826055 0.63085981 -1.07926364
[61] -0.17234820 0.82628398 -0.64334720 0.87199185 1.45010879 -0.11656597
[67] 0.23611047 -0.40289121 1.02185662 0.44080198 -0.98394440 -0.35536935
[73] -1.04860402 0.47313115 -1.98012096 0.40833997 -0.73087657 0.87533633
[79] -0.06745004 -0.51703977 0.82916982 1.94841476 -1.07821685 0.20579781
[85] -1.13496423 -0.12237210 -1.25933684 0.81421018 -0.39754751 -1.12308516
[91] -0.95328410 1.91065282 0.31874195 -1.99279247 -1.50632767 0.72551098
[97] -1.95772320 0.85986552 -0.51347947 0.67339457
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] -1.43005392 -1.06254889 -1.33908377 0.67412609 0.86042477 0.20530428
[7] -0.12613618 0.18232360 -0.59158429 -1.37738792 -0.47667344 0.21062821
[13] -1.07970948 -0.76752848 -1.02612292 -0.85402295 -0.37255026 -0.70144278
[19] -0.45570336 -1.32050719 -0.48455264 0.98794220 2.13578438 0.35351042
[25] 0.78857958 0.06953550 -1.16836335 -0.80259072 3.44749872 -0.73836080
[31] 0.60483082 0.75043598 2.41863291 -0.72627038 0.08194523 -0.30694708
[37] -0.53175787 0.70691792 -0.28716086 -0.14643420 0.45323509 2.19516040
[43] -0.74101643 -1.36870443 -0.39506221 -0.05122619 -1.62330585 0.84494821
[49] 0.60220952 -0.68531037 1.44626354 1.18244260 -1.99020087 -2.13599301
[55] -0.33312725 0.23014343 -0.30548586 -0.62826055 0.63085981 -1.07926364
[61] -0.17234820 0.82628398 -0.64334720 0.87199185 1.45010879 -0.11656597
[67] 0.23611047 -0.40289121 1.02185662 0.44080198 -0.98394440 -0.35536935
[73] -1.04860402 0.47313115 -1.98012096 0.40833997 -0.73087657 0.87533633
[79] -0.06745004 -0.51703977 0.82916982 1.94841476 -1.07821685 0.20579781
[85] -1.13496423 -0.12237210 -1.25933684 0.81421018 -0.39754751 -1.12308516
[91] -0.95328410 1.91065282 0.31874195 -1.99279247 -1.50632767 0.72551098
[97] -1.95772320 0.85986552 -0.51347947 0.67339457
> colMin(tmp)
[1] -1.43005392 -1.06254889 -1.33908377 0.67412609 0.86042477 0.20530428
[7] -0.12613618 0.18232360 -0.59158429 -1.37738792 -0.47667344 0.21062821
[13] -1.07970948 -0.76752848 -1.02612292 -0.85402295 -0.37255026 -0.70144278
[19] -0.45570336 -1.32050719 -0.48455264 0.98794220 2.13578438 0.35351042
[25] 0.78857958 0.06953550 -1.16836335 -0.80259072 3.44749872 -0.73836080
[31] 0.60483082 0.75043598 2.41863291 -0.72627038 0.08194523 -0.30694708
[37] -0.53175787 0.70691792 -0.28716086 -0.14643420 0.45323509 2.19516040
[43] -0.74101643 -1.36870443 -0.39506221 -0.05122619 -1.62330585 0.84494821
[49] 0.60220952 -0.68531037 1.44626354 1.18244260 -1.99020087 -2.13599301
[55] -0.33312725 0.23014343 -0.30548586 -0.62826055 0.63085981 -1.07926364
[61] -0.17234820 0.82628398 -0.64334720 0.87199185 1.45010879 -0.11656597
[67] 0.23611047 -0.40289121 1.02185662 0.44080198 -0.98394440 -0.35536935
[73] -1.04860402 0.47313115 -1.98012096 0.40833997 -0.73087657 0.87533633
[79] -0.06745004 -0.51703977 0.82916982 1.94841476 -1.07821685 0.20579781
[85] -1.13496423 -0.12237210 -1.25933684 0.81421018 -0.39754751 -1.12308516
[91] -0.95328410 1.91065282 0.31874195 -1.99279247 -1.50632767 0.72551098
[97] -1.95772320 0.85986552 -0.51347947 0.67339457
> colMedians(tmp)
[1] -1.43005392 -1.06254889 -1.33908377 0.67412609 0.86042477 0.20530428
[7] -0.12613618 0.18232360 -0.59158429 -1.37738792 -0.47667344 0.21062821
[13] -1.07970948 -0.76752848 -1.02612292 -0.85402295 -0.37255026 -0.70144278
[19] -0.45570336 -1.32050719 -0.48455264 0.98794220 2.13578438 0.35351042
[25] 0.78857958 0.06953550 -1.16836335 -0.80259072 3.44749872 -0.73836080
[31] 0.60483082 0.75043598 2.41863291 -0.72627038 0.08194523 -0.30694708
[37] -0.53175787 0.70691792 -0.28716086 -0.14643420 0.45323509 2.19516040
[43] -0.74101643 -1.36870443 -0.39506221 -0.05122619 -1.62330585 0.84494821
[49] 0.60220952 -0.68531037 1.44626354 1.18244260 -1.99020087 -2.13599301
[55] -0.33312725 0.23014343 -0.30548586 -0.62826055 0.63085981 -1.07926364
[61] -0.17234820 0.82628398 -0.64334720 0.87199185 1.45010879 -0.11656597
[67] 0.23611047 -0.40289121 1.02185662 0.44080198 -0.98394440 -0.35536935
[73] -1.04860402 0.47313115 -1.98012096 0.40833997 -0.73087657 0.87533633
[79] -0.06745004 -0.51703977 0.82916982 1.94841476 -1.07821685 0.20579781
[85] -1.13496423 -0.12237210 -1.25933684 0.81421018 -0.39754751 -1.12308516
[91] -0.95328410 1.91065282 0.31874195 -1.99279247 -1.50632767 0.72551098
[97] -1.95772320 0.85986552 -0.51347947 0.67339457
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -1.430054 -1.062549 -1.339084 0.6741261 0.8604248 0.2053043 -0.1261362
[2,] -1.430054 -1.062549 -1.339084 0.6741261 0.8604248 0.2053043 -0.1261362
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.1823236 -0.5915843 -1.377388 -0.4766734 0.2106282 -1.079709 -0.7675285
[2,] 0.1823236 -0.5915843 -1.377388 -0.4766734 0.2106282 -1.079709 -0.7675285
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -1.026123 -0.854023 -0.3725503 -0.7014428 -0.4557034 -1.320507 -0.4845526
[2,] -1.026123 -0.854023 -0.3725503 -0.7014428 -0.4557034 -1.320507 -0.4845526
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.9879422 2.135784 0.3535104 0.7885796 0.0695355 -1.168363 -0.8025907
[2,] 0.9879422 2.135784 0.3535104 0.7885796 0.0695355 -1.168363 -0.8025907
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 3.447499 -0.7383608 0.6048308 0.750436 2.418633 -0.7262704 0.08194523
[2,] 3.447499 -0.7383608 0.6048308 0.750436 2.418633 -0.7262704 0.08194523
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -0.3069471 -0.5317579 0.7069179 -0.2871609 -0.1464342 0.4532351 2.19516
[2,] -0.3069471 -0.5317579 0.7069179 -0.2871609 -0.1464342 0.4532351 2.19516
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.7410164 -1.368704 -0.3950622 -0.05122619 -1.623306 0.8449482 0.6022095
[2,] -0.7410164 -1.368704 -0.3950622 -0.05122619 -1.623306 0.8449482 0.6022095
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -0.6853104 1.446264 1.182443 -1.990201 -2.135993 -0.3331272 0.2301434
[2,] -0.6853104 1.446264 1.182443 -1.990201 -2.135993 -0.3331272 0.2301434
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -0.3054859 -0.6282606 0.6308598 -1.079264 -0.1723482 0.826284 -0.6433472
[2,] -0.3054859 -0.6282606 0.6308598 -1.079264 -0.1723482 0.826284 -0.6433472
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.8719918 1.450109 -0.116566 0.2361105 -0.4028912 1.021857 0.440802
[2,] 0.8719918 1.450109 -0.116566 0.2361105 -0.4028912 1.021857 0.440802
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -0.9839444 -0.3553694 -1.048604 0.4731311 -1.980121 0.40834 -0.7308766
[2,] -0.9839444 -0.3553694 -1.048604 0.4731311 -1.980121 0.40834 -0.7308766
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.8753363 -0.06745004 -0.5170398 0.8291698 1.948415 -1.078217 0.2057978
[2,] 0.8753363 -0.06745004 -0.5170398 0.8291698 1.948415 -1.078217 0.2057978
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -1.134964 -0.1223721 -1.259337 0.8142102 -0.3975475 -1.123085 -0.9532841
[2,] -1.134964 -0.1223721 -1.259337 0.8142102 -0.3975475 -1.123085 -0.9532841
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 1.910653 0.318742 -1.992792 -1.506328 0.725511 -1.957723 0.8598655
[2,] 1.910653 0.318742 -1.992792 -1.506328 0.725511 -1.957723 0.8598655
[,99] [,100]
[1,] -0.5134795 0.6733946
[2,] -0.5134795 0.6733946
>
>
> Max(tmp2)
[1] 2.117983
> Min(tmp2)
[1] -3.56878
> mean(tmp2)
[1] -0.1044022
> Sum(tmp2)
[1] -10.44022
> Var(tmp2)
[1] 0.950732
>
> rowMeans(tmp2)
[1] -1.700995e-01 -1.397626e+00 7.983791e-01 -3.908791e-01 -1.510049e+00
[6] -8.915340e-01 7.149807e-01 4.222027e-01 -1.768552e-01 -1.897894e-02
[11] -6.955095e-01 -1.784935e+00 1.623653e+00 -1.418964e+00 7.201805e-01
[16] 3.965414e-01 -1.266830e+00 7.733708e-01 1.579746e+00 6.544821e-01
[21] -5.833932e-01 1.974495e+00 1.081543e+00 7.828448e-01 5.989989e-02
[26] 2.855754e-01 -4.734362e-01 9.750865e-01 -9.732691e-01 2.859960e-01
[31] -2.127845e-01 -2.266339e-01 4.421499e-01 -4.077315e-01 -8.915807e-02
[36] -8.235276e-01 -3.315506e-01 2.117983e+00 6.379205e-01 -1.203581e+00
[41] -9.798754e-01 -9.303492e-01 6.595000e-01 -3.907162e-01 6.354305e-01
[46] 1.527187e+00 2.806945e-01 5.860732e-01 3.702054e-01 -3.341883e-01
[51] 4.804779e-01 -3.948805e-01 -7.741939e-01 8.443188e-01 2.953133e-01
[56] -2.142959e-02 -2.453386e-01 -1.387181e+00 1.212000e+00 -3.492982e-01
[61] -1.489229e+00 -1.669160e+00 -1.088342e-01 1.369291e+00 5.079356e-03
[66] -1.673806e+00 -8.597320e-01 -9.958964e-01 -6.249871e-01 -4.521293e-01
[71] 9.600009e-01 -3.568780e+00 -4.332945e-01 -2.973140e-01 -1.767601e+00
[76] 8.249182e-01 1.674598e-01 -6.790238e-01 -9.167846e-01 -1.208187e+00
[81] 9.024156e-05 9.379851e-01 -8.512729e-01 -1.982568e-01 -1.891544e+00
[86] 1.979279e-01 1.173015e+00 -1.601507e-01 6.616128e-01 4.762449e-01
[91] -5.536731e-01 -3.537824e-01 1.127651e+00 -1.111129e+00 1.812459e-01
[96] -1.514821e+00 3.735870e-01 1.061909e+00 1.012024e+00 4.567852e-02
> rowSums(tmp2)
[1] -1.700995e-01 -1.397626e+00 7.983791e-01 -3.908791e-01 -1.510049e+00
[6] -8.915340e-01 7.149807e-01 4.222027e-01 -1.768552e-01 -1.897894e-02
[11] -6.955095e-01 -1.784935e+00 1.623653e+00 -1.418964e+00 7.201805e-01
[16] 3.965414e-01 -1.266830e+00 7.733708e-01 1.579746e+00 6.544821e-01
[21] -5.833932e-01 1.974495e+00 1.081543e+00 7.828448e-01 5.989989e-02
[26] 2.855754e-01 -4.734362e-01 9.750865e-01 -9.732691e-01 2.859960e-01
[31] -2.127845e-01 -2.266339e-01 4.421499e-01 -4.077315e-01 -8.915807e-02
[36] -8.235276e-01 -3.315506e-01 2.117983e+00 6.379205e-01 -1.203581e+00
[41] -9.798754e-01 -9.303492e-01 6.595000e-01 -3.907162e-01 6.354305e-01
[46] 1.527187e+00 2.806945e-01 5.860732e-01 3.702054e-01 -3.341883e-01
[51] 4.804779e-01 -3.948805e-01 -7.741939e-01 8.443188e-01 2.953133e-01
[56] -2.142959e-02 -2.453386e-01 -1.387181e+00 1.212000e+00 -3.492982e-01
[61] -1.489229e+00 -1.669160e+00 -1.088342e-01 1.369291e+00 5.079356e-03
[66] -1.673806e+00 -8.597320e-01 -9.958964e-01 -6.249871e-01 -4.521293e-01
[71] 9.600009e-01 -3.568780e+00 -4.332945e-01 -2.973140e-01 -1.767601e+00
[76] 8.249182e-01 1.674598e-01 -6.790238e-01 -9.167846e-01 -1.208187e+00
[81] 9.024156e-05 9.379851e-01 -8.512729e-01 -1.982568e-01 -1.891544e+00
[86] 1.979279e-01 1.173015e+00 -1.601507e-01 6.616128e-01 4.762449e-01
[91] -5.536731e-01 -3.537824e-01 1.127651e+00 -1.111129e+00 1.812459e-01
[96] -1.514821e+00 3.735870e-01 1.061909e+00 1.012024e+00 4.567852e-02
> rowVars(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowSd(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowMax(tmp2)
[1] -1.700995e-01 -1.397626e+00 7.983791e-01 -3.908791e-01 -1.510049e+00
[6] -8.915340e-01 7.149807e-01 4.222027e-01 -1.768552e-01 -1.897894e-02
[11] -6.955095e-01 -1.784935e+00 1.623653e+00 -1.418964e+00 7.201805e-01
[16] 3.965414e-01 -1.266830e+00 7.733708e-01 1.579746e+00 6.544821e-01
[21] -5.833932e-01 1.974495e+00 1.081543e+00 7.828448e-01 5.989989e-02
[26] 2.855754e-01 -4.734362e-01 9.750865e-01 -9.732691e-01 2.859960e-01
[31] -2.127845e-01 -2.266339e-01 4.421499e-01 -4.077315e-01 -8.915807e-02
[36] -8.235276e-01 -3.315506e-01 2.117983e+00 6.379205e-01 -1.203581e+00
[41] -9.798754e-01 -9.303492e-01 6.595000e-01 -3.907162e-01 6.354305e-01
[46] 1.527187e+00 2.806945e-01 5.860732e-01 3.702054e-01 -3.341883e-01
[51] 4.804779e-01 -3.948805e-01 -7.741939e-01 8.443188e-01 2.953133e-01
[56] -2.142959e-02 -2.453386e-01 -1.387181e+00 1.212000e+00 -3.492982e-01
[61] -1.489229e+00 -1.669160e+00 -1.088342e-01 1.369291e+00 5.079356e-03
[66] -1.673806e+00 -8.597320e-01 -9.958964e-01 -6.249871e-01 -4.521293e-01
[71] 9.600009e-01 -3.568780e+00 -4.332945e-01 -2.973140e-01 -1.767601e+00
[76] 8.249182e-01 1.674598e-01 -6.790238e-01 -9.167846e-01 -1.208187e+00
[81] 9.024156e-05 9.379851e-01 -8.512729e-01 -1.982568e-01 -1.891544e+00
[86] 1.979279e-01 1.173015e+00 -1.601507e-01 6.616128e-01 4.762449e-01
[91] -5.536731e-01 -3.537824e-01 1.127651e+00 -1.111129e+00 1.812459e-01
[96] -1.514821e+00 3.735870e-01 1.061909e+00 1.012024e+00 4.567852e-02
> rowMin(tmp2)
[1] -1.700995e-01 -1.397626e+00 7.983791e-01 -3.908791e-01 -1.510049e+00
[6] -8.915340e-01 7.149807e-01 4.222027e-01 -1.768552e-01 -1.897894e-02
[11] -6.955095e-01 -1.784935e+00 1.623653e+00 -1.418964e+00 7.201805e-01
[16] 3.965414e-01 -1.266830e+00 7.733708e-01 1.579746e+00 6.544821e-01
[21] -5.833932e-01 1.974495e+00 1.081543e+00 7.828448e-01 5.989989e-02
[26] 2.855754e-01 -4.734362e-01 9.750865e-01 -9.732691e-01 2.859960e-01
[31] -2.127845e-01 -2.266339e-01 4.421499e-01 -4.077315e-01 -8.915807e-02
[36] -8.235276e-01 -3.315506e-01 2.117983e+00 6.379205e-01 -1.203581e+00
[41] -9.798754e-01 -9.303492e-01 6.595000e-01 -3.907162e-01 6.354305e-01
[46] 1.527187e+00 2.806945e-01 5.860732e-01 3.702054e-01 -3.341883e-01
[51] 4.804779e-01 -3.948805e-01 -7.741939e-01 8.443188e-01 2.953133e-01
[56] -2.142959e-02 -2.453386e-01 -1.387181e+00 1.212000e+00 -3.492982e-01
[61] -1.489229e+00 -1.669160e+00 -1.088342e-01 1.369291e+00 5.079356e-03
[66] -1.673806e+00 -8.597320e-01 -9.958964e-01 -6.249871e-01 -4.521293e-01
[71] 9.600009e-01 -3.568780e+00 -4.332945e-01 -2.973140e-01 -1.767601e+00
[76] 8.249182e-01 1.674598e-01 -6.790238e-01 -9.167846e-01 -1.208187e+00
[81] 9.024156e-05 9.379851e-01 -8.512729e-01 -1.982568e-01 -1.891544e+00
[86] 1.979279e-01 1.173015e+00 -1.601507e-01 6.616128e-01 4.762449e-01
[91] -5.536731e-01 -3.537824e-01 1.127651e+00 -1.111129e+00 1.812459e-01
[96] -1.514821e+00 3.735870e-01 1.061909e+00 1.012024e+00 4.567852e-02
>
> colMeans(tmp2)
[1] -0.1044022
> colSums(tmp2)
[1] -10.44022
> colVars(tmp2)
[1] 0.950732
> colSd(tmp2)
[1] 0.9750549
> colMax(tmp2)
[1] 2.117983
> colMin(tmp2)
[1] -3.56878
> colMedians(tmp2)
[1] -0.1344924
> colRanges(tmp2)
[,1]
[1,] -3.568780
[2,] 2.117983
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] 2.3726942 -0.7753888 -2.9660243 -1.9047910 1.0726043 -0.8343036
[7] -4.0915400 1.3275896 2.0660821 -8.8765106
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.20724580
[2,] -0.34427188
[3,] 0.02491546
[4,] 0.46532542
[5,] 2.61470933
>
> rowApply(tmp,sum)
[1] 2.7990656 -0.6049611 1.1176679 -1.7502578 -1.0669696 -2.2002256
[7] -0.9603540 2.0431718 -5.3834578 -6.6032676
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 7 6 6 6 4 9 3 10 5 6
[2,] 8 3 9 8 2 8 8 3 1 8
[3,] 6 7 3 5 8 1 2 9 6 3
[4,] 10 9 4 1 9 4 1 2 7 9
[5,] 2 8 8 9 7 2 4 7 8 7
[6,] 1 2 10 10 5 7 7 4 2 4
[7,] 9 1 1 7 6 6 6 8 10 2
[8,] 3 5 2 3 10 5 10 5 4 10
[9,] 5 10 7 4 3 10 5 6 9 5
[10,] 4 4 5 2 1 3 9 1 3 1
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 0.30032550 0.77824736 0.07833314 2.04580563 1.85267765 3.00926412
[7] 3.35801282 1.59877786 1.22108552 0.26210454 0.80975809 -1.20399655
[13] -3.25476758 3.13719272 -0.80933577 1.86562637 3.37186766 2.23007419
[19] 1.00031673 -0.07028547
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.8843718
[2,] -0.6731470
[3,] 0.4155725
[4,] 0.6147273
[5,] 0.8275444
>
> rowApply(tmp,sum)
[1] 5.7029712 5.3370625 -1.1924894 11.0344876 0.6990527
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 12 15 16 3 4
[2,] 8 17 3 6 16
[3,] 20 3 8 10 12
[4,] 18 8 7 9 19
[5,] 1 10 19 17 10
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.4155725 0.038215269 1.34398778 1.1885393 -0.8914244 0.09959662
[2,] 0.8275444 1.354005136 -1.43120531 -0.3119674 0.1434301 2.58685357
[3,] 0.6147273 -1.344348336 -0.24523199 -0.5066622 1.3791118 -0.53693532
[4,] -0.8843718 -0.009691903 0.39109747 0.3860180 1.3871903 1.31480027
[5,] -0.6731470 0.740067189 0.01968517 1.2898778 -0.1656301 -0.45505101
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.99684877 0.91226979 -0.30697748 1.24514002 -0.2135092 0.24105501
[2,] 0.19703914 -0.28047765 -0.38391642 1.74296018 0.5574608 -0.73906957
[3,] 0.02136665 -0.07655800 0.08200774 -1.49506499 1.1488140 0.06095761
[4,] 0.17217225 1.13081384 2.00775451 0.04844396 0.6404745 -1.01706407
[5,] 1.97058601 -0.08727012 -0.17778283 -1.27937463 -1.3234821 0.25012448
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.6615317 0.56433667 -0.7447203 0.4045561 -0.1335697 0.6920081
[2,] -1.6560654 0.45937255 2.9245850 -0.7312140 0.8062784 1.1375128
[3,] 0.1439199 1.40765292 -1.8590608 -0.8079817 0.6040084 -0.8583746
[4,] -1.3274892 -0.09863103 -0.7183344 2.8251866 1.1215982 1.4246304
[5,] -1.0766645 0.80446161 -0.4118052 0.1750793 0.9735523 -0.1657025
[,19] [,20]
[1,] -0.3241412 -0.48634434
[2,] -0.3918951 -1.47416883
[3,] 1.1221258 -0.04696354
[4,] 0.9638287 1.27606103
[5,] -0.3696014 0.66113021
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 654 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 566 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 -0.6375389 -2.173006 -0.4591961 -1.382354 -1.856363 0.01026112 0.9366904
col8 col9 col10 col11 col12 col13 col14
row1 0.4779869 -0.4665185 -0.09963238 1.40072 0.3329165 0.1502016 0.6395316
col15 col16 col17 col18 col19 col20
row1 -1.185877 -1.353638 0.6612386 0.5588698 -1.785651 1.343538
> tmp[,"col10"]
col10
row1 -0.09963238
row2 -1.08273751
row3 -1.00906049
row4 -0.22740504
row5 -2.07283804
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 -0.6375389 -2.17300585 -0.4591961 -1.3823540 -1.8563633 0.01026112
row5 0.4049494 0.04924446 0.4116856 0.2678276 -0.7968215 1.31560341
col7 col8 col9 col10 col11 col12 col13
row1 0.9366904 0.4779869 -0.4665185 -0.09963238 1.4007196 0.3329165 0.1502016
row5 -0.6996724 0.1082674 -1.5408081 -2.07283804 -0.9608861 1.6082509 1.2054027
col14 col15 col16 col17 col18 col19 col20
row1 0.6395316 -1.185877 -1.35363784 0.6612386 0.5588698 -1.78565082 1.343538
row5 0.6163790 1.127536 -0.03283985 2.5818109 -2.1220639 0.01759554 1.037641
> tmp[,c("col6","col20")]
col6 col20
row1 0.01026112 1.34353842
row2 1.29151844 -0.49477074
row3 -0.19925417 0.02248057
row4 -0.96094076 -1.60830737
row5 1.31560341 1.03764116
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.01026112 1.343538
row5 1.31560341 1.037641
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.50176 49.69019 48.4067 49.72611 50.19354 103.9034 49.19656 50.87248
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.07852 50.6383 49.28114 50.58598 49.7735 50.04925 51.32352 49.83255
col17 col18 col19 col20
row1 48.90977 51.10244 48.22002 106.9566
> tmp[,"col10"]
col10
row1 50.63830
row2 31.36428
row3 28.37180
row4 29.38258
row5 50.62493
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.50176 49.69019 48.4067 49.72611 50.19354 103.9034 49.19656 50.87248
row5 49.06832 48.98691 50.6760 50.30790 48.63281 105.0469 49.66731 49.40348
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.07852 50.63830 49.28114 50.58598 49.77350 50.04925 51.32352 49.83255
row5 48.99098 50.62493 49.75524 52.00740 50.53419 49.38691 49.23050 49.93362
col17 col18 col19 col20
row1 48.90977 51.10244 48.22002 106.9566
row5 51.62625 48.81355 50.24776 103.9596
> tmp[,c("col6","col20")]
col6 col20
row1 103.90340 106.95658
row2 74.76623 75.08195
row3 76.60979 76.88693
row4 76.44182 73.95273
row5 105.04692 103.95962
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 103.9034 106.9566
row5 105.0469 103.9596
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 103.9034 106.9566
row5 105.0469 103.9596
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.9913022
[2,] 0.0760323
[3,] -1.2034094
[4,] 0.2790740
[5,] -0.5499238
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.1407099 -0.3882910
[2,] 0.4155168 0.7673597
[3,] 0.9914963 -1.4282940
[4,] -0.6480649 -0.8524134
[5,] -0.4376567 1.2430411
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.1246940 1.1374002
[2,] -2.0034234 0.2001076
[3,] -0.3276706 0.5916083
[4,] 0.5456904 -1.9754408
[5,] 0.1541333 2.1001727
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.124694
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.124694
[2,] -2.003423
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6]
row3 -1.039634 -0.1092909 0.3039786 -0.8490561 0.28903205 0.7052605
row1 -1.199066 1.1363109 -0.1569031 0.5955052 -0.02185543 -1.5433401
[,7] [,8] [,9] [,10] [,11] [,12] [,13]
row3 1.3231669 -1.145619 1.243873 1.8927549 -1.485401 -0.4611124 -0.1533536
row1 0.4388214 -2.232687 -1.123725 0.8471912 1.606438 0.5820173 -0.2408033
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 -0.1211721 0.08717274 0.5533179 -1.572656 1.355439 1.539631 -0.2967114
row1 -1.3726437 0.47628681 -0.0829202 -1.702241 -1.976716 -1.109068 1.0898640
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.187045 0.6577503 0.8974188 -1.728554 0.02823415 0.3356992 -2.750518
[,8] [,9] [,10]
row2 1.480776 0.9634296 -0.3086222
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.08393177 -1.250108 -0.327245 0.2477638 0.2447457 1.327232 0.9972341
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 0.9057554 0.7288376 0.3070051 0.2880922 0.2819805 1.715376 0.4926124
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.07979107 -0.7090734 -2.280539 1.620384 -0.667457 -0.6162265
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> colnames(tmp) <- NULL
> rownames(tmp) <- NULL
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
> dimnames(tmp) <- NULL
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
> dimnames(tmp) <- NULL
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
NULL
>
> dimnames(tmp) <- list(NULL,c(colnames(tmp,do.NULL=FALSE)))
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
>
> ###
> ### Testing logical indexing
> ###
> ###
>
> tmp <- createBufferedMatrix(230,15)
> tmp[1:230,1:15] <- rnorm(230*15)
> x <-tmp[1:230,1:15]
>
> for (rep in 1:10){
+ which.cols <- sample(c(TRUE,FALSE),15,replace=T)
+ which.rows <- sample(c(TRUE,FALSE),230,replace=T)
+
+ if (!all(tmp[which.rows,which.cols] == x[which.rows,which.cols])){
+ stop("No agreement when logical indexing\n")
+ }
+
+ if (!all(subBufferedMatrix(tmp,,which.cols)[,1:sum(which.cols)] == x[,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix cols\n")
+ }
+ if (!all(subBufferedMatrix(tmp,which.rows,)[1:sum(which.rows),] == x[which.rows,])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows\n")
+ }
+
+
+ if (!all(subBufferedMatrix(tmp,which.rows,which.cols)[1:sum(which.rows),1:sum(which.cols)]== x[which.rows,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows and columns\n")
+ }
+ }
>
>
> ##
> ## Test the ReadOnlyMode
> ##
>
> ReadOnlyMode(tmp)
<pointer: 0x5c96b4f5d670>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM20e5527b9a69f1"
[2] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM20e5522267a833"
[3] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM20e552d020fa1"
[4] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM20e5523f2b990e"
[5] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM20e5521ceb9920"
[6] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM20e55243b4315c"
[7] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM20e5528d5f0ce"
[8] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM20e5523fe00172"
[9] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM20e5526746cb69"
[10] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM20e5523f15bcb3"
[11] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM20e55250429844"
[12] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM20e5527b9e50d6"
[13] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM20e5522c8fc40e"
[14] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM20e5522c67614d"
[15] "/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests/BM20e55220591402"
>
>
> ### testing coercion functions
> ###
>
> tmp <- as(tmp,"matrix")
> tmp <- as(tmp,"BufferedMatrix")
>
>
>
> ### testing whether can move storage from one location to another
>
> MoveStorageDirectory(tmp,"NewDirectory",full.path=FALSE)
<pointer: 0x5c96b50d12e0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x5c96b50d12e0>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.24-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x5c96b50d12e0>
> rowMedians(tmp)
[1] -0.7156915307 0.1921229740 0.0797124475 0.0608450593 0.2279284126
[6] -0.4928999302 0.0687184037 0.3422761073 -0.1930910034 -0.1695536848
[11] 0.2257656286 0.4951413612 0.0720080856 0.4705310370 0.0576428986
[16] -0.5231248046 0.1082352977 -0.3763357360 -0.2039091683 0.2853559070
[21] 0.0259515313 -0.2257386386 -0.1194541673 0.4770758126 0.3970127747
[26] -0.1375297824 0.1537207922 0.0191849825 0.1003954930 0.0094861631
[31] 0.5742443272 -0.2420016343 -0.4016926564 0.2605506916 0.3520101466
[36] 0.0445685780 -0.7406868029 -0.0793406868 0.0861560025 0.7240399244
[41] 0.1375537168 -0.2337859341 0.0413044925 -0.2451483591 -0.4524620006
[46] -0.2499116924 -0.1515119629 0.1129126848 -0.3111962218 0.0606807823
[51] -0.7231760607 0.4446495899 -0.6545629366 0.5988763378 -0.2606806191
[56] -0.4882789240 -0.2942786328 -0.2419838833 0.3392308657 -0.4922777665
[61] -0.5519957923 0.3202758324 0.0085827322 -0.2611132178 -0.2054288908
[66] -0.1524774356 0.1543989990 0.3031107854 0.1768497321 0.0524948623
[71] 0.1707409093 0.6164445637 0.4549650310 -0.3028406090 -0.1243735528
[76] 0.1933555976 0.1537347428 -0.3223479881 -0.3995873852 -0.0954833673
[81] 0.0692274277 0.0968559454 0.1745169675 -0.1629303373 0.4213583334
[86] 0.3872403855 0.2879713023 -0.3558654143 -0.7761802755 0.4556760355
[91] -0.4466696036 0.3901622768 -0.1051312056 -0.2873722468 0.0531841041
[96] 0.2895050817 0.2094698652 -0.5487185754 -0.0715179711 -0.4489465709
[101] -0.1044875659 0.4199323060 0.8238311232 -0.4109308205 -0.0502884138
[106] 0.4105393705 0.6225690733 0.3252228765 0.2552471477 -0.1356490181
[111] 0.2988245044 0.3591182406 -0.0034217022 -0.0809817913 0.2024342531
[116] -0.0058709974 0.1461583888 0.1759775228 0.2289595151 0.1854205942
[121] -0.3503506071 -0.1913212932 0.2544137144 -0.0856812119 0.3834944714
[126] -0.0163576984 0.5052833716 -0.1084532112 0.4112784934 -0.2326298008
[131] 0.2535677912 0.1617390413 0.0931280280 0.0592273139 -0.0615145452
[136] 0.1770734392 0.2217209663 0.0363625207 0.5287914792 0.2313896905
[141] 0.0638856357 -0.4607799621 0.3525087177 -0.4685601302 0.1914935976
[146] -0.3668025058 -0.0269483468 -0.3096033614 -0.1207014131 -0.3096313502
[151] 0.6213874883 -0.6911003326 -0.1330467022 -0.3463978389 0.6094713472
[156] -0.3753544598 0.0389198299 0.3278739070 0.1435919627 -0.3868022275
[161] 0.0844921678 0.2796109460 -0.5307663556 -0.2229866734 -0.2283664566
[166] 0.3851387576 -0.0041975573 -0.2187196833 -0.0115814789 -0.0740841067
[171] 0.4565796739 0.2460218293 -0.0067828838 -0.5644842787 0.0982185008
[176] -0.4612836591 -0.1898517697 0.5378434625 -0.5018944515 0.0052774506
[181] 0.2912256267 0.7005702611 -0.4008309671 0.2267229026 0.2495401133
[186] 0.1012497542 0.2429328729 0.0670644072 0.5909201958 0.5808429795
[191] 0.1077224883 -0.5971137833 -0.1007679088 -0.3679010063 0.3179275994
[196] 0.3898972373 0.1378284434 0.3453313758 -0.0093676052 0.0931558360
[201] -0.3352690343 -0.6918731400 0.0230355766 -0.0978426351 -0.3879790544
[206] -0.4165114567 0.0660026612 -0.1037618552 0.0678111313 -0.2015878096
[211] 0.0741578103 0.0008828509 -0.6662098533 0.0165271538 0.1697607268
[216] -0.0092985297 -0.2996143089 -0.2537409681 0.0164432055 -0.1527134286
[221] -0.0470704806 0.0152736610 0.0861497447 0.3067683542 0.1982521566
[226] -0.1614079803 0.1810099291 -0.0062821888 0.3143102744 -0.1870013219
>
> proc.time()
user system elapsed
1.244 0.689 1.920
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> prefix <- "dbmtest"
> directory <- getwd()
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x5c38ecbd5520>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x5c38ecbd5520>
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x5c38ecbd5520>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000 0.000000 0.000000 0.000000 0.000000
<pointer: 0x5c38ecbd5520>
> rm(P)
>
> #P <- .Call("R_bm_Destroy",P)
> #.Call("R_bm_Destroy",P)
> #.Call("R_bm_Test_C",P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 0
Buffer Rows: 1
Buffer Cols: 1
Printing Values
<pointer: 0x5c38ec77ef60>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5c38ec77ef60>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 1
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000
0.000000
0.000000
0.000000
0.000000
<pointer: 0x5c38ec77ef60>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5c38ec77ef60>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x5c38ec77ef60>
> rm(P)
>
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5c38ed328b40>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5c38ed328b40>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x5c38ed328b40>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5c38ed328b40>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x5c38ed328b40>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x5c38ed328b40>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x5c38ed328b40>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x5c38ed328b40>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x5c38ed328b40>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5c38ed365bc0>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x5c38ed365bc0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5c38ed365bc0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5c38ed365bc0>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile20e5993fc7d5fa" "BufferedMatrixFile20e5997138af91"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile20e5993fc7d5fa" "BufferedMatrixFile20e5997138af91"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5c38ed2ff000>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5c38ed2ff000>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5c38ed2ff000>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5c38ed2ff000>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x5c38ed2ff000>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x5c38ed2ff000>
> .Call("R_bm_isRowMode",P)
[1] FALSE
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5c38ec432e30>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5c38ec432e30>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5c38ec432e30>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x5c38ec432e30>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x5c38eca5ca50>
> .Call("R_bm_getValue",P,3,3)
[1] 6
>
> .Call("R_bm_getValue",P,100000,10000)
[1] NA
> .Call("R_bm_setValue",P,3,3,12345.0)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 12345.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x5c38eca5ca50>
> rm(P)
>
> proc.time()
user system elapsed
0.244 0.039 0.273
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.236 0.051 0.274