Ben Bolstad
| Snapshot Date: 2026-03-24 13:45 -0400 (Tue, 24 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_22 |
| git_last_commit: d2ce144 |
| git_last_commit_date: 2025-10-29 09:58:55 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-03-25 11:57 -0400 (Wed, 25 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4893 |
| 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 257/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.74.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| 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: 1.74.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BufferedMatrix_1.74.0.tar.gz |
| StartedAt: 2026-03-24 21:31:02 -0400 (Tue, 24 Mar 2026) |
| EndedAt: 2026-03-24 21:31:27 -0400 (Tue, 24 Mar 2026) |
| EllapsedTime: 24.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BufferedMatrix_1.74.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.74.0’
* 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 ... NOTE
Note: information on .o files is not available
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.74.0’
** 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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-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-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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
0.240 0.047 0.277
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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-3.22-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 478284 25.6 1046725 56 639600 34.2
Vcells 884773 6.8 8388608 64 2081613 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] "Tue Mar 24 21:31:17 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] "Tue Mar 24 21:31:17 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: 0x6189610e8370>
>
>
>
> 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] "Tue Mar 24 21:31:17 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] "Tue Mar 24 21:31:18 2026"
>
> ColMode(tmp2)
<pointer: 0x6189610e8370>
>
>
>
> ### 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,] 97.8034111 1.2881626 0.04657506 0.2791457
[2,] -0.4894736 1.5542927 -0.53096511 -0.4879666
[3,] 0.3435990 0.2807863 0.10780140 -1.2515783
[4,] -0.8402863 0.1705307 -0.69342457 1.3872088
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-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,] 97.8034111 1.2881626 0.04657506 0.2791457
[2,] 0.4894736 1.5542927 0.53096511 0.4879666
[3,] 0.3435990 0.2807863 0.10780140 1.2515783
[4,] 0.8402863 0.1705307 0.69342457 1.3872088
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-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,] 9.8895607 1.1349725 0.2158126 0.5283424
[2,] 0.6996239 1.2467128 0.7286735 0.6985461
[3,] 0.5861732 0.5298927 0.3283312 1.1187396
[4,] 0.9166713 0.4129536 0.8327212 1.1777983
>
> 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-3.22-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,] 221.69902 37.63789 27.20470 30.56257
[2,] 32.48571 39.02142 32.81770 32.47343
[3,] 31.20533 30.57971 28.39111 37.43897
[4,] 35.00700 29.30007 34.02064 38.16519
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x6189620e49b0>
> exp(tmp5)
<pointer: 0x6189620e49b0>
> log(tmp5,2)
<pointer: 0x6189620e49b0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 461.4375
> Min(tmp5)
[1] 53.35009
> mean(tmp5)
[1] 72.68664
> Sum(tmp5)
[1] 14537.33
> Var(tmp5)
[1] 829.9633
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 90.18036 71.72484 70.68496 70.53472 69.61524 69.09960 70.51346 69.72001
[9] 70.97423 73.81901
> rowSums(tmp5)
[1] 1803.607 1434.497 1413.699 1410.694 1392.305 1381.992 1410.269 1394.400
[9] 1419.485 1476.380
> rowVars(tmp5)
[1] 7697.99398 98.64944 63.21072 77.11149 65.82938 78.80197
[7] 56.31932 71.48940 51.25815 57.76056
> rowSd(tmp5)
[1] 87.738213 9.932242 7.950517 8.781315 8.113531 8.877048 7.504620
[8] 8.455141 7.159480 7.600037
> rowMax(tmp5)
[1] 461.43746 88.05993 85.10991 94.20509 84.14668 93.68608 80.58276
[8] 83.30421 80.78779 85.01736
> rowMin(tmp5)
[1] 56.62302 55.32647 57.07309 54.50268 55.43843 58.91513 58.63501 53.35009
[9] 55.00435 55.62530
>
> colMeans(tmp5)
[1] 104.78355 69.51637 67.33707 72.28334 75.73371 70.77021 76.24260
[8] 75.88662 71.18014 67.57355 71.21569 72.33106 66.21847 70.88378
[15] 71.23791 71.83231 70.67266 68.58662 71.43671 68.01050
> colSums(tmp5)
[1] 1047.8355 695.1637 673.3707 722.8334 757.3371 707.7021 762.4260
[8] 758.8662 711.8014 675.7355 712.1569 723.3106 662.1847 708.8378
[15] 712.3791 718.3231 706.7266 685.8662 714.3671 680.1050
> colVars(tmp5)
[1] 15754.13051 71.52130 43.75623 42.27898 48.98847 102.08974
[7] 56.35256 103.44471 77.93155 71.10971 34.71235 48.05643
[13] 21.41744 35.53121 58.11228 123.30989 23.83122 50.98575
[19] 135.39006 84.23872
> colSd(tmp5)
[1] 125.515459 8.457026 6.614849 6.502229 6.999177 10.103947
[7] 7.506834 10.170777 8.827885 8.432657 5.891718 6.932275
[13] 4.627898 5.960806 7.623141 11.104499 4.881723 7.140430
[19] 11.635723 9.178165
> colMax(tmp5)
[1] 461.43746 81.21797 77.69279 79.43585 82.47785 83.30421 88.05993
[8] 93.68608 80.85543 80.78779 83.19829 86.02894 73.12469 78.95220
[15] 83.58329 94.20509 77.60300 76.05610 88.54962 86.21986
> colMin(tmp5)
[1] 55.00435 60.98425 56.62302 63.59065 61.23110 54.50268 66.65917 62.47207
[9] 56.27212 55.32647 63.31654 62.70780 60.08351 60.98446 60.61172 55.62530
[17] 63.77377 58.78620 53.35009 59.69345
>
>
> ### 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] 90.18036 71.72484 70.68496 70.53472 69.61524 NA 70.51346 69.72001
[9] 70.97423 73.81901
> rowSums(tmp5)
[1] 1803.607 1434.497 1413.699 1410.694 1392.305 NA 1410.269 1394.400
[9] 1419.485 1476.380
> rowVars(tmp5)
[1] 7697.99398 98.64944 63.21072 77.11149 65.82938 47.82926
[7] 56.31932 71.48940 51.25815 57.76056
> rowSd(tmp5)
[1] 87.738213 9.932242 7.950517 8.781315 8.113531 6.915870 7.504620
[8] 8.455141 7.159480 7.600037
> rowMax(tmp5)
[1] 461.43746 88.05993 85.10991 94.20509 84.14668 NA 80.58276
[8] 83.30421 80.78779 85.01736
> rowMin(tmp5)
[1] 56.62302 55.32647 57.07309 54.50268 55.43843 NA 58.63501 53.35009
[9] 55.00435 55.62530
>
> colMeans(tmp5)
[1] 104.78355 69.51637 67.33707 72.28334 75.73371 70.77021 76.24260
[8] NA 71.18014 67.57355 71.21569 72.33106 66.21847 70.88378
[15] 71.23791 71.83231 70.67266 68.58662 71.43671 68.01050
> colSums(tmp5)
[1] 1047.8355 695.1637 673.3707 722.8334 757.3371 707.7021 762.4260
[8] NA 711.8014 675.7355 712.1569 723.3106 662.1847 708.8378
[15] 712.3791 718.3231 706.7266 685.8662 714.3671 680.1050
> colVars(tmp5)
[1] 15754.13051 71.52130 43.75623 42.27898 48.98847 102.08974
[7] 56.35256 NA 77.93155 71.10971 34.71235 48.05643
[13] 21.41744 35.53121 58.11228 123.30989 23.83122 50.98575
[19] 135.39006 84.23872
> colSd(tmp5)
[1] 125.515459 8.457026 6.614849 6.502229 6.999177 10.103947
[7] 7.506834 NA 8.827885 8.432657 5.891718 6.932275
[13] 4.627898 5.960806 7.623141 11.104499 4.881723 7.140430
[19] 11.635723 9.178165
> colMax(tmp5)
[1] 461.43746 81.21797 77.69279 79.43585 82.47785 83.30421 88.05993
[8] NA 80.85543 80.78779 83.19829 86.02894 73.12469 78.95220
[15] 83.58329 94.20509 77.60300 76.05610 88.54962 86.21986
> colMin(tmp5)
[1] 55.00435 60.98425 56.62302 63.59065 61.23110 54.50268 66.65917 NA
[9] 56.27212 55.32647 63.31654 62.70780 60.08351 60.98446 60.61172 55.62530
[17] 63.77377 58.78620 53.35009 59.69345
>
> Max(tmp5,na.rm=TRUE)
[1] 461.4375
> Min(tmp5,na.rm=TRUE)
[1] 53.35009
> mean(tmp5,na.rm=TRUE)
[1] 72.58112
> Sum(tmp5,na.rm=TRUE)
[1] 14443.64
> Var(tmp5,na.rm=TRUE)
[1] 831.9167
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.18036 71.72484 70.68496 70.53472 69.61524 67.80557 70.51346 69.72001
[9] 70.97423 73.81901
> rowSums(tmp5,na.rm=TRUE)
[1] 1803.607 1434.497 1413.699 1410.694 1392.305 1288.306 1410.269 1394.400
[9] 1419.485 1476.380
> rowVars(tmp5,na.rm=TRUE)
[1] 7697.99398 98.64944 63.21072 77.11149 65.82938 47.82926
[7] 56.31932 71.48940 51.25815 57.76056
> rowSd(tmp5,na.rm=TRUE)
[1] 87.738213 9.932242 7.950517 8.781315 8.113531 6.915870 7.504620
[8] 8.455141 7.159480 7.600037
> rowMax(tmp5,na.rm=TRUE)
[1] 461.43746 88.05993 85.10991 94.20509 84.14668 88.54962 80.58276
[8] 83.30421 80.78779 85.01736
> rowMin(tmp5,na.rm=TRUE)
[1] 56.62302 55.32647 57.07309 54.50268 55.43843 58.91513 58.63501 53.35009
[9] 55.00435 55.62530
>
> colMeans(tmp5,na.rm=TRUE)
[1] 104.78355 69.51637 67.33707 72.28334 75.73371 70.77021 76.24260
[8] 73.90890 71.18014 67.57355 71.21569 72.33106 66.21847 70.88378
[15] 71.23791 71.83231 70.67266 68.58662 71.43671 68.01050
> colSums(tmp5,na.rm=TRUE)
[1] 1047.8355 695.1637 673.3707 722.8334 757.3371 707.7021 762.4260
[8] 665.1801 711.8014 675.7355 712.1569 723.3106 662.1847 708.8378
[15] 712.3791 718.3231 706.7266 685.8662 714.3671 680.1050
> colVars(tmp5,na.rm=TRUE)
[1] 15754.13051 71.52130 43.75623 42.27898 48.98847 102.08974
[7] 56.35256 72.37240 77.93155 71.10971 34.71235 48.05643
[13] 21.41744 35.53121 58.11228 123.30989 23.83122 50.98575
[19] 135.39006 84.23872
> colSd(tmp5,na.rm=TRUE)
[1] 125.515459 8.457026 6.614849 6.502229 6.999177 10.103947
[7] 7.506834 8.507197 8.827885 8.432657 5.891718 6.932275
[13] 4.627898 5.960806 7.623141 11.104499 4.881723 7.140430
[19] 11.635723 9.178165
> colMax(tmp5,na.rm=TRUE)
[1] 461.43746 81.21797 77.69279 79.43585 82.47785 83.30421 88.05993
[8] 89.16579 80.85543 80.78779 83.19829 86.02894 73.12469 78.95220
[15] 83.58329 94.20509 77.60300 76.05610 88.54962 86.21986
> colMin(tmp5,na.rm=TRUE)
[1] 55.00435 60.98425 56.62302 63.59065 61.23110 54.50268 66.65917 62.47207
[9] 56.27212 55.32647 63.31654 62.70780 60.08351 60.98446 60.61172 55.62530
[17] 63.77377 58.78620 53.35009 59.69345
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.18036 71.72484 70.68496 70.53472 69.61524 NaN 70.51346 69.72001
[9] 70.97423 73.81901
> rowSums(tmp5,na.rm=TRUE)
[1] 1803.607 1434.497 1413.699 1410.694 1392.305 0.000 1410.269 1394.400
[9] 1419.485 1476.380
> rowVars(tmp5,na.rm=TRUE)
[1] 7697.99398 98.64944 63.21072 77.11149 65.82938 NA
[7] 56.31932 71.48940 51.25815 57.76056
> rowSd(tmp5,na.rm=TRUE)
[1] 87.738213 9.932242 7.950517 8.781315 8.113531 NA 7.504620
[8] 8.455141 7.159480 7.600037
> rowMax(tmp5,na.rm=TRUE)
[1] 461.43746 88.05993 85.10991 94.20509 84.14668 NA 80.58276
[8] 83.30421 80.78779 85.01736
> rowMin(tmp5,na.rm=TRUE)
[1] 56.62302 55.32647 57.07309 54.50268 55.43843 NA 58.63501 53.35009
[9] 55.00435 55.62530
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 108.34000 70.23607 67.68397 73.05127 76.65196 72.01400 77.16535
[8] NaN 71.30303 67.99800 72.09337 72.46985 65.45111 70.57979
[15] 71.21715 73.26755 71.43921 68.36360 69.53528 68.93462
> colSums(tmp5,na.rm=TRUE)
[1] 975.0600 632.1246 609.1557 657.4614 689.8677 648.1260 694.4882 0.0000
[9] 641.7273 611.9820 648.8403 652.2286 589.0600 635.2181 640.9543 659.4080
[17] 642.9529 615.2724 625.8175 620.4116
> colVars(tmp5,na.rm=TRUE)
[1] 17581.10250 74.63444 47.87193 40.92955 45.62619 97.44712
[7] 53.81746 NA 87.50308 77.97166 30.38520 53.84680
[13] 17.47018 38.93297 65.37147 115.54953 20.19974 56.79941
[19] 111.63998 85.16115
> colSd(tmp5,na.rm=TRUE)
[1] 132.593750 8.639123 6.918955 6.397621 6.754716 9.871531
[7] 7.336039 NA 9.354308 8.830156 5.512277 7.338038
[13] 4.179735 6.239629 8.085262 10.749397 4.494412 7.536539
[19] 10.565982 9.228280
> colMax(tmp5,na.rm=TRUE)
[1] 461.43746 81.21797 77.69279 79.43585 82.47785 83.30421 88.05993
[8] -Inf 80.85543 80.78779 83.19829 86.02894 70.44767 78.95220
[15] 83.58329 94.20509 77.60300 76.05610 85.01736 86.21986
> colMin(tmp5,na.rm=TRUE)
[1] 55.00435 60.98425 56.62302 63.59065 61.23110 54.50268 66.65917 Inf
[9] 56.27212 55.32647 64.54846 62.70780 60.08351 60.98446 60.61172 55.62530
[17] 64.82928 58.78620 53.35009 60.67876
>
>
>
>
> 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] 214.6986 441.5531 233.7404 242.8120 381.5763 223.7354 147.8907 259.3255
[9] 163.4824 300.4168
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 214.6986 441.5531 233.7404 242.8120 381.5763 223.7354 147.8907 259.3255
[9] 163.4824 300.4168
>
>
>
> 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] 0.000000e+00 -1.421085e-13 0.000000e+00 0.000000e+00 2.842171e-13
[6] -2.273737e-13 5.684342e-14 1.136868e-13 5.684342e-14 -1.136868e-13
[11] -8.526513e-14 1.136868e-13 0.000000e+00 1.705303e-13 -1.989520e-13
[16] 2.273737e-13 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00
>
>
>
>
>
>
>
>
>
>
> ## 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)
+ }
5 11
2 16
4 13
2 12
6 18
7 9
5 2
4 18
1 15
3 7
10 6
2 1
6 17
2 15
2 10
10 11
3 9
4 9
8 10
9 20
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] 3.117615
> Min(tmp)
[1] -3.713633
> mean(tmp)
[1] -0.19932
> Sum(tmp)
[1] -19.932
> Var(tmp)
[1] 1.490932
>
> rowMeans(tmp)
[1] -0.19932
> rowSums(tmp)
[1] -19.932
> rowVars(tmp)
[1] 1.490932
> rowSd(tmp)
[1] 1.221037
> rowMax(tmp)
[1] 3.117615
> rowMin(tmp)
[1] -3.713633
>
> colMeans(tmp)
[1] 0.316036764 1.883240241 1.293713983 0.928871450 -3.116362739
[6] 0.261088929 0.924329809 -1.328320009 0.226154401 -0.333275930
[11] 0.430674381 0.109207459 2.138973649 -1.211297553 -1.472928125
[16] -0.615580256 -1.221185903 -2.103130150 -0.006521739 -1.065841429
[21] -0.343149665 -1.731226567 0.196641135 0.677089070 1.119039862
[26] 0.925116501 0.230253313 0.622430009 -2.478482683 -1.106182282
[31] -0.385763830 0.227997221 -0.196461798 -0.645999760 -1.195245416
[36] 0.151150386 0.504811370 -2.499513856 -1.049679368 -0.315736456
[41] -0.190823382 1.189206796 -0.058506692 0.586415208 -2.083957171
[46] -0.866472555 -2.828476930 -1.182349380 1.104825673 1.343649046
[51] 0.978911276 -0.320105158 1.572532818 0.391963560 -0.664874879
[56] -3.713632540 -0.109582469 -1.186563957 0.540241735 0.287283279
[61] -1.732323551 2.718279910 1.485459107 -1.783904971 -1.074703055
[66] 0.661700428 1.426149738 0.098800051 -0.961646189 -2.493086405
[71] 3.117614517 0.571347073 -1.990064306 -0.566615285 -1.272535352
[76] -0.334267695 0.931877888 0.291214317 0.068332830 -0.813141098
[81] -0.320345283 0.434617215 -1.248115456 -1.141878126 -0.493125820
[86] 0.220901804 -0.603253803 -0.180208512 0.787074209 0.350169222
[91] 0.876444345 0.369484379 -0.375141845 -1.656901328 0.140867635
[96] -0.676550800 0.077911520 1.168813299 0.403563210 0.050570643
> colSums(tmp)
[1] 0.316036764 1.883240241 1.293713983 0.928871450 -3.116362739
[6] 0.261088929 0.924329809 -1.328320009 0.226154401 -0.333275930
[11] 0.430674381 0.109207459 2.138973649 -1.211297553 -1.472928125
[16] -0.615580256 -1.221185903 -2.103130150 -0.006521739 -1.065841429
[21] -0.343149665 -1.731226567 0.196641135 0.677089070 1.119039862
[26] 0.925116501 0.230253313 0.622430009 -2.478482683 -1.106182282
[31] -0.385763830 0.227997221 -0.196461798 -0.645999760 -1.195245416
[36] 0.151150386 0.504811370 -2.499513856 -1.049679368 -0.315736456
[41] -0.190823382 1.189206796 -0.058506692 0.586415208 -2.083957171
[46] -0.866472555 -2.828476930 -1.182349380 1.104825673 1.343649046
[51] 0.978911276 -0.320105158 1.572532818 0.391963560 -0.664874879
[56] -3.713632540 -0.109582469 -1.186563957 0.540241735 0.287283279
[61] -1.732323551 2.718279910 1.485459107 -1.783904971 -1.074703055
[66] 0.661700428 1.426149738 0.098800051 -0.961646189 -2.493086405
[71] 3.117614517 0.571347073 -1.990064306 -0.566615285 -1.272535352
[76] -0.334267695 0.931877888 0.291214317 0.068332830 -0.813141098
[81] -0.320345283 0.434617215 -1.248115456 -1.141878126 -0.493125820
[86] 0.220901804 -0.603253803 -0.180208512 0.787074209 0.350169222
[91] 0.876444345 0.369484379 -0.375141845 -1.656901328 0.140867635
[96] -0.676550800 0.077911520 1.168813299 0.403563210 0.050570643
> 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] 0.316036764 1.883240241 1.293713983 0.928871450 -3.116362739
[6] 0.261088929 0.924329809 -1.328320009 0.226154401 -0.333275930
[11] 0.430674381 0.109207459 2.138973649 -1.211297553 -1.472928125
[16] -0.615580256 -1.221185903 -2.103130150 -0.006521739 -1.065841429
[21] -0.343149665 -1.731226567 0.196641135 0.677089070 1.119039862
[26] 0.925116501 0.230253313 0.622430009 -2.478482683 -1.106182282
[31] -0.385763830 0.227997221 -0.196461798 -0.645999760 -1.195245416
[36] 0.151150386 0.504811370 -2.499513856 -1.049679368 -0.315736456
[41] -0.190823382 1.189206796 -0.058506692 0.586415208 -2.083957171
[46] -0.866472555 -2.828476930 -1.182349380 1.104825673 1.343649046
[51] 0.978911276 -0.320105158 1.572532818 0.391963560 -0.664874879
[56] -3.713632540 -0.109582469 -1.186563957 0.540241735 0.287283279
[61] -1.732323551 2.718279910 1.485459107 -1.783904971 -1.074703055
[66] 0.661700428 1.426149738 0.098800051 -0.961646189 -2.493086405
[71] 3.117614517 0.571347073 -1.990064306 -0.566615285 -1.272535352
[76] -0.334267695 0.931877888 0.291214317 0.068332830 -0.813141098
[81] -0.320345283 0.434617215 -1.248115456 -1.141878126 -0.493125820
[86] 0.220901804 -0.603253803 -0.180208512 0.787074209 0.350169222
[91] 0.876444345 0.369484379 -0.375141845 -1.656901328 0.140867635
[96] -0.676550800 0.077911520 1.168813299 0.403563210 0.050570643
> colMin(tmp)
[1] 0.316036764 1.883240241 1.293713983 0.928871450 -3.116362739
[6] 0.261088929 0.924329809 -1.328320009 0.226154401 -0.333275930
[11] 0.430674381 0.109207459 2.138973649 -1.211297553 -1.472928125
[16] -0.615580256 -1.221185903 -2.103130150 -0.006521739 -1.065841429
[21] -0.343149665 -1.731226567 0.196641135 0.677089070 1.119039862
[26] 0.925116501 0.230253313 0.622430009 -2.478482683 -1.106182282
[31] -0.385763830 0.227997221 -0.196461798 -0.645999760 -1.195245416
[36] 0.151150386 0.504811370 -2.499513856 -1.049679368 -0.315736456
[41] -0.190823382 1.189206796 -0.058506692 0.586415208 -2.083957171
[46] -0.866472555 -2.828476930 -1.182349380 1.104825673 1.343649046
[51] 0.978911276 -0.320105158 1.572532818 0.391963560 -0.664874879
[56] -3.713632540 -0.109582469 -1.186563957 0.540241735 0.287283279
[61] -1.732323551 2.718279910 1.485459107 -1.783904971 -1.074703055
[66] 0.661700428 1.426149738 0.098800051 -0.961646189 -2.493086405
[71] 3.117614517 0.571347073 -1.990064306 -0.566615285 -1.272535352
[76] -0.334267695 0.931877888 0.291214317 0.068332830 -0.813141098
[81] -0.320345283 0.434617215 -1.248115456 -1.141878126 -0.493125820
[86] 0.220901804 -0.603253803 -0.180208512 0.787074209 0.350169222
[91] 0.876444345 0.369484379 -0.375141845 -1.656901328 0.140867635
[96] -0.676550800 0.077911520 1.168813299 0.403563210 0.050570643
> colMedians(tmp)
[1] 0.316036764 1.883240241 1.293713983 0.928871450 -3.116362739
[6] 0.261088929 0.924329809 -1.328320009 0.226154401 -0.333275930
[11] 0.430674381 0.109207459 2.138973649 -1.211297553 -1.472928125
[16] -0.615580256 -1.221185903 -2.103130150 -0.006521739 -1.065841429
[21] -0.343149665 -1.731226567 0.196641135 0.677089070 1.119039862
[26] 0.925116501 0.230253313 0.622430009 -2.478482683 -1.106182282
[31] -0.385763830 0.227997221 -0.196461798 -0.645999760 -1.195245416
[36] 0.151150386 0.504811370 -2.499513856 -1.049679368 -0.315736456
[41] -0.190823382 1.189206796 -0.058506692 0.586415208 -2.083957171
[46] -0.866472555 -2.828476930 -1.182349380 1.104825673 1.343649046
[51] 0.978911276 -0.320105158 1.572532818 0.391963560 -0.664874879
[56] -3.713632540 -0.109582469 -1.186563957 0.540241735 0.287283279
[61] -1.732323551 2.718279910 1.485459107 -1.783904971 -1.074703055
[66] 0.661700428 1.426149738 0.098800051 -0.961646189 -2.493086405
[71] 3.117614517 0.571347073 -1.990064306 -0.566615285 -1.272535352
[76] -0.334267695 0.931877888 0.291214317 0.068332830 -0.813141098
[81] -0.320345283 0.434617215 -1.248115456 -1.141878126 -0.493125820
[86] 0.220901804 -0.603253803 -0.180208512 0.787074209 0.350169222
[91] 0.876444345 0.369484379 -0.375141845 -1.656901328 0.140867635
[96] -0.676550800 0.077911520 1.168813299 0.403563210 0.050570643
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.3160368 1.88324 1.293714 0.9288714 -3.116363 0.2610889 0.9243298
[2,] 0.3160368 1.88324 1.293714 0.9288714 -3.116363 0.2610889 0.9243298
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -1.32832 0.2261544 -0.3332759 0.4306744 0.1092075 2.138974 -1.211298
[2,] -1.32832 0.2261544 -0.3332759 0.4306744 0.1092075 2.138974 -1.211298
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -1.472928 -0.6155803 -1.221186 -2.10313 -0.006521739 -1.065841 -0.3431497
[2,] -1.472928 -0.6155803 -1.221186 -2.10313 -0.006521739 -1.065841 -0.3431497
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -1.731227 0.1966411 0.6770891 1.11904 0.9251165 0.2302533 0.62243
[2,] -1.731227 0.1966411 0.6770891 1.11904 0.9251165 0.2302533 0.62243
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -2.478483 -1.106182 -0.3857638 0.2279972 -0.1964618 -0.6459998 -1.195245
[2,] -2.478483 -1.106182 -0.3857638 0.2279972 -0.1964618 -0.6459998 -1.195245
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.1511504 0.5048114 -2.499514 -1.049679 -0.3157365 -0.1908234 1.189207
[2,] 0.1511504 0.5048114 -2.499514 -1.049679 -0.3157365 -0.1908234 1.189207
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.05850669 0.5864152 -2.083957 -0.8664726 -2.828477 -1.182349 1.104826
[2,] -0.05850669 0.5864152 -2.083957 -0.8664726 -2.828477 -1.182349 1.104826
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 1.343649 0.9789113 -0.3201052 1.572533 0.3919636 -0.6648749 -3.713633
[2,] 1.343649 0.9789113 -0.3201052 1.572533 0.3919636 -0.6648749 -3.713633
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -0.1095825 -1.186564 0.5402417 0.2872833 -1.732324 2.71828 1.485459
[2,] -0.1095825 -1.186564 0.5402417 0.2872833 -1.732324 2.71828 1.485459
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -1.783905 -1.074703 0.6617004 1.42615 0.09880005 -0.9616462 -2.493086
[2,] -1.783905 -1.074703 0.6617004 1.42615 0.09880005 -0.9616462 -2.493086
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 3.117615 0.5713471 -1.990064 -0.5666153 -1.272535 -0.3342677 0.9318779
[2,] 3.117615 0.5713471 -1.990064 -0.5666153 -1.272535 -0.3342677 0.9318779
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.2912143 0.06833283 -0.8131411 -0.3203453 0.4346172 -1.248115 -1.141878
[2,] 0.2912143 0.06833283 -0.8131411 -0.3203453 0.4346172 -1.248115 -1.141878
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -0.4931258 0.2209018 -0.6032538 -0.1802085 0.7870742 0.3501692 0.8764443
[2,] -0.4931258 0.2209018 -0.6032538 -0.1802085 0.7870742 0.3501692 0.8764443
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 0.3694844 -0.3751418 -1.656901 0.1408676 -0.6765508 0.07791152 1.168813
[2,] 0.3694844 -0.3751418 -1.656901 0.1408676 -0.6765508 0.07791152 1.168813
[,99] [,100]
[1,] 0.4035632 0.05057064
[2,] 0.4035632 0.05057064
>
>
> Max(tmp2)
[1] 2.696745
> Min(tmp2)
[1] -3.677736
> mean(tmp2)
[1] 0.02287255
> Sum(tmp2)
[1] 2.287255
> Var(tmp2)
[1] 0.9893844
>
> rowMeans(tmp2)
[1] -1.183034389 -1.880228610 1.051249226 0.569373245 -0.441098511
[6] 1.380674961 -1.178489465 0.404350638 -0.669081045 -0.256555141
[11] -0.583208469 2.052003635 0.652455492 1.208383690 -0.768284073
[16] 0.344364676 -0.508027654 -0.443555816 0.643713480 -0.533159690
[21] 0.069154864 -1.067112355 1.346277599 -0.669527186 -0.187613553
[26] 0.062146419 -0.131762031 0.325231659 0.012461235 0.150478688
[31] -1.278602175 -1.091835324 1.015357247 -0.816408214 0.999655279
[36] -0.894243128 0.573874045 -0.043108847 0.391507160 0.329388220
[41] 0.066797678 0.513966875 -0.445482117 0.336369596 -0.890995190
[46] 1.008441899 -0.928550359 0.275092889 -0.878114615 -0.766180088
[51] 0.167956434 1.036391794 -0.475764537 -0.337955293 -1.167641951
[56] -1.456232050 1.119253758 -1.543255432 0.559674322 0.866522867
[61] 0.933489623 0.495719173 -0.235569747 -0.198986137 1.666604706
[66] -1.247463327 -1.092932146 1.282251588 -0.162181040 -1.520219622
[71] 2.696745257 0.227924761 -1.471520989 0.757254041 -0.350334759
[76] 1.986359375 1.236582920 -0.676719101 0.608182045 -0.201714331
[81] -0.381061980 0.890059252 0.401532053 1.038549001 0.218719535
[86] 1.485286638 -1.588019637 0.248827584 -0.700744560 0.720861077
[91] -0.021777486 1.275481584 -3.677736429 0.551833739 -0.144597804
[96] 0.690735616 -0.004894583 1.149187688 -1.205410211 0.589489316
> rowSums(tmp2)
[1] -1.183034389 -1.880228610 1.051249226 0.569373245 -0.441098511
[6] 1.380674961 -1.178489465 0.404350638 -0.669081045 -0.256555141
[11] -0.583208469 2.052003635 0.652455492 1.208383690 -0.768284073
[16] 0.344364676 -0.508027654 -0.443555816 0.643713480 -0.533159690
[21] 0.069154864 -1.067112355 1.346277599 -0.669527186 -0.187613553
[26] 0.062146419 -0.131762031 0.325231659 0.012461235 0.150478688
[31] -1.278602175 -1.091835324 1.015357247 -0.816408214 0.999655279
[36] -0.894243128 0.573874045 -0.043108847 0.391507160 0.329388220
[41] 0.066797678 0.513966875 -0.445482117 0.336369596 -0.890995190
[46] 1.008441899 -0.928550359 0.275092889 -0.878114615 -0.766180088
[51] 0.167956434 1.036391794 -0.475764537 -0.337955293 -1.167641951
[56] -1.456232050 1.119253758 -1.543255432 0.559674322 0.866522867
[61] 0.933489623 0.495719173 -0.235569747 -0.198986137 1.666604706
[66] -1.247463327 -1.092932146 1.282251588 -0.162181040 -1.520219622
[71] 2.696745257 0.227924761 -1.471520989 0.757254041 -0.350334759
[76] 1.986359375 1.236582920 -0.676719101 0.608182045 -0.201714331
[81] -0.381061980 0.890059252 0.401532053 1.038549001 0.218719535
[86] 1.485286638 -1.588019637 0.248827584 -0.700744560 0.720861077
[91] -0.021777486 1.275481584 -3.677736429 0.551833739 -0.144597804
[96] 0.690735616 -0.004894583 1.149187688 -1.205410211 0.589489316
> 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] -1.183034389 -1.880228610 1.051249226 0.569373245 -0.441098511
[6] 1.380674961 -1.178489465 0.404350638 -0.669081045 -0.256555141
[11] -0.583208469 2.052003635 0.652455492 1.208383690 -0.768284073
[16] 0.344364676 -0.508027654 -0.443555816 0.643713480 -0.533159690
[21] 0.069154864 -1.067112355 1.346277599 -0.669527186 -0.187613553
[26] 0.062146419 -0.131762031 0.325231659 0.012461235 0.150478688
[31] -1.278602175 -1.091835324 1.015357247 -0.816408214 0.999655279
[36] -0.894243128 0.573874045 -0.043108847 0.391507160 0.329388220
[41] 0.066797678 0.513966875 -0.445482117 0.336369596 -0.890995190
[46] 1.008441899 -0.928550359 0.275092889 -0.878114615 -0.766180088
[51] 0.167956434 1.036391794 -0.475764537 -0.337955293 -1.167641951
[56] -1.456232050 1.119253758 -1.543255432 0.559674322 0.866522867
[61] 0.933489623 0.495719173 -0.235569747 -0.198986137 1.666604706
[66] -1.247463327 -1.092932146 1.282251588 -0.162181040 -1.520219622
[71] 2.696745257 0.227924761 -1.471520989 0.757254041 -0.350334759
[76] 1.986359375 1.236582920 -0.676719101 0.608182045 -0.201714331
[81] -0.381061980 0.890059252 0.401532053 1.038549001 0.218719535
[86] 1.485286638 -1.588019637 0.248827584 -0.700744560 0.720861077
[91] -0.021777486 1.275481584 -3.677736429 0.551833739 -0.144597804
[96] 0.690735616 -0.004894583 1.149187688 -1.205410211 0.589489316
> rowMin(tmp2)
[1] -1.183034389 -1.880228610 1.051249226 0.569373245 -0.441098511
[6] 1.380674961 -1.178489465 0.404350638 -0.669081045 -0.256555141
[11] -0.583208469 2.052003635 0.652455492 1.208383690 -0.768284073
[16] 0.344364676 -0.508027654 -0.443555816 0.643713480 -0.533159690
[21] 0.069154864 -1.067112355 1.346277599 -0.669527186 -0.187613553
[26] 0.062146419 -0.131762031 0.325231659 0.012461235 0.150478688
[31] -1.278602175 -1.091835324 1.015357247 -0.816408214 0.999655279
[36] -0.894243128 0.573874045 -0.043108847 0.391507160 0.329388220
[41] 0.066797678 0.513966875 -0.445482117 0.336369596 -0.890995190
[46] 1.008441899 -0.928550359 0.275092889 -0.878114615 -0.766180088
[51] 0.167956434 1.036391794 -0.475764537 -0.337955293 -1.167641951
[56] -1.456232050 1.119253758 -1.543255432 0.559674322 0.866522867
[61] 0.933489623 0.495719173 -0.235569747 -0.198986137 1.666604706
[66] -1.247463327 -1.092932146 1.282251588 -0.162181040 -1.520219622
[71] 2.696745257 0.227924761 -1.471520989 0.757254041 -0.350334759
[76] 1.986359375 1.236582920 -0.676719101 0.608182045 -0.201714331
[81] -0.381061980 0.890059252 0.401532053 1.038549001 0.218719535
[86] 1.485286638 -1.588019637 0.248827584 -0.700744560 0.720861077
[91] -0.021777486 1.275481584 -3.677736429 0.551833739 -0.144597804
[96] 0.690735616 -0.004894583 1.149187688 -1.205410211 0.589489316
>
> colMeans(tmp2)
[1] 0.02287255
> colSums(tmp2)
[1] 2.287255
> colVars(tmp2)
[1] 0.9893844
> colSd(tmp2)
[1] 0.994678
> colMax(tmp2)
[1] 2.696745
> colMin(tmp2)
[1] -3.677736
> colMedians(tmp2)
[1] 0.06447205
> colRanges(tmp2)
[,1]
[1,] -3.677736
[2,] 2.696745
>
> 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] -2.8995159 0.6650059 5.2232437 1.5972328 -0.2614368 -6.8086459
[7] -1.4234771 5.2886617 0.3918920 1.4688550
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.3382085
[2,] -1.0396877
[3,] -0.6301094
[4,] 0.3892783
[5,] 1.1683904
>
> rowApply(tmp,sum)
[1] 3.4940447 5.5239693 -0.9204739 -5.0128249 0.9042780 -5.0676575
[7] 5.4811449 -0.1682996 -3.3032802 2.3109146
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 3 6 2 5 4 10 5 7 3 1
[2,] 2 8 7 8 8 5 4 4 10 2
[3,] 10 7 4 10 6 1 6 10 8 8
[4,] 7 4 6 4 7 9 1 6 5 7
[5,] 6 5 5 6 1 6 7 8 1 10
[6,] 4 2 1 1 9 2 2 1 6 3
[7,] 5 3 9 2 5 4 8 3 7 6
[8,] 9 10 10 3 10 8 3 5 2 9
[9,] 1 9 8 7 2 3 9 9 4 4
[10,] 8 1 3 9 3 7 10 2 9 5
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 1.4152669 1.4709072 3.3530551 1.2195784 -1.1819831 2.2589827
[7] -1.3918401 0.7697653 -2.2586616 -1.4040265 2.8491639 0.7694653
[13] 0.4219500 -1.2728439 1.2138260 -1.4603095 -1.7271103 1.6606298
[19] -0.1186446 2.0915200
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.49712238
[2,] 0.07191767
[3,] 0.09900663
[4,] 0.13654560
[5,] 1.60491937
>
> rowApply(tmp,sum)
[1] 1.7655574 4.9861655 -0.7497904 1.5521678 1.1245909
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 10 9 7 9 20
[2,] 2 15 13 13 15
[3,] 17 12 18 8 16
[4,] 3 4 19 7 19
[5,] 7 5 2 19 10
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.07191767 -1.0671541 0.78982467 -0.6447088 -0.1485345 0.245481508
[2,] 0.13654560 1.0233608 0.49837632 -0.6035765 -0.5631137 1.036575456
[3,] -0.49712238 0.2533194 1.30846987 1.5011991 -1.3830120 0.406220630
[4,] 0.09900663 0.5160396 -0.02868343 -0.1670266 1.1177548 0.564525624
[5,] 1.60491937 0.7453414 0.78506769 1.1336913 -0.2050776 0.006179495
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -1.2976384 1.6762175 0.3176343 -0.5404507 0.93947936 0.8700740
[2,] 0.5795330 1.2057369 1.0320012 0.3989353 0.02077604 -0.6370724
[3,] 0.2401877 -1.0876369 -0.7712984 -2.5826230 0.46795956 1.7183164
[4,] -0.4758789 -0.7200097 -2.1671788 0.3723004 1.07696032 -0.4757768
[5,] -0.4380435 -0.3045425 -0.6698199 0.9478115 0.34398862 -0.7060759
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.1974947 -0.6145480 0.5341975 0.04237927 -0.6162232 0.04642736
[2,] -0.1312512 -1.1470475 1.3485812 0.14972454 -0.8297560 1.10863483
[3,] -0.4771392 0.1531756 -0.5640332 -1.00434131 0.8694539 0.76932108
[4,] 0.6450453 0.5477163 -1.1279639 0.35199652 -0.6008719 0.52904796
[5,] 0.1878004 -0.2121403 1.0230445 -1.00006849 -0.5497131 -0.79280141
[,19] [,20]
[1,] 0.60881005 0.35487723
[2,] -0.22502728 0.58422890
[3,] -0.04336356 -0.02684366
[4,] 0.33380299 1.16136133
[5,] -0.79286681 0.01789624
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-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-3.22-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-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 565 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-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 0.5747489 1.396297 0.564528 1.831638 -0.1172354 -0.3417916 1.712568
col8 col9 col10 col11 col12 col13 col14
row1 0.6319314 0.4720538 -2.28236 0.3983027 1.029921 -1.591349 -2.496218
col15 col16 col17 col18 col19 col20
row1 0.2695184 -1.405935 0.6330266 -0.6868307 0.2735756 -0.1706008
> tmp[,"col10"]
col10
row1 -2.2823598
row2 -1.1188858
row3 1.1424093
row4 0.6431758
row5 -1.4704353
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 0.5747489 1.3962971 0.5645280 1.8316378 -0.1172354 -0.3417916
row5 -0.7611302 -0.1291203 -0.2249333 0.8664564 0.8505494 1.6048665
col7 col8 col9 col10 col11 col12 col13
row1 1.7125683 0.6319314 0.472053831 -2.282360 0.39830269 1.029921 -1.591349
row5 -0.5018058 0.4186284 -0.002926187 -1.470435 0.04388613 -1.045607 0.960067
col14 col15 col16 col17 col18 col19
row1 -2.496218 0.2695184 -1.4059346 0.6330266 -0.6868307 0.27357559
row5 1.537016 0.1873494 0.1619864 -0.4366525 1.1091324 -0.07921675
col20
row1 -0.1706008
row5 0.6666293
> tmp[,c("col6","col20")]
col6 col20
row1 -0.3417916 -0.1706008
row2 -0.4974301 0.6933254
row3 -0.6519809 -1.4978080
row4 -0.6133431 0.4768426
row5 1.6048665 0.6666293
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.3417916 -0.1706008
row5 1.6048665 0.6666293
>
>
>
>
> 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 51.18761 49.64498 49.14033 49.16942 48.66002 104.4495 49.65264 49.3659
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.33918 51.30681 51.59 49.81637 49.95847 50.35442 50.72481 49.68026
col17 col18 col19 col20
row1 49.39146 51.44749 49.42359 104.932
> tmp[,"col10"]
col10
row1 51.30681
row2 29.03472
row3 29.76731
row4 30.75401
row5 49.73577
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 51.18761 49.64498 49.14033 49.16942 48.66002 104.4495 49.65264 49.36590
row5 47.24641 49.36349 50.45000 50.87489 48.54159 105.7155 49.33189 49.07115
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.33918 51.30681 51.59000 49.81637 49.95847 50.35442 50.72481 49.68026
row5 50.17052 49.73577 48.45328 50.36196 52.97222 49.21557 49.58822 51.14023
col17 col18 col19 col20
row1 49.39146 51.44749 49.42359 104.9320
row5 50.05365 49.63550 50.29756 104.4318
> tmp[,c("col6","col20")]
col6 col20
row1 104.44946 104.93198
row2 75.60088 75.26968
row3 75.63572 75.34729
row4 75.21537 76.21852
row5 105.71549 104.43179
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.4495 104.9320
row5 105.7155 104.4318
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.4495 104.9320
row5 105.7155 104.4318
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.7987841
[2,] 1.4291924
[3,] 0.9578570
[4,] -1.0525941
[5,] -0.9543497
> tmp[,c("col17","col7")]
col17 col7
[1,] 1.37598844 -0.7618312
[2,] -0.45266860 -1.2870213
[3,] 0.08601536 2.3535276
[4,] -0.79504103 0.3957885
[5,] -1.32365053 0.5276792
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.3712317 -0.1749676
[2,] 0.2797962 1.7077267
[3,] 2.1815054 0.9839427
[4,] -0.6602560 0.8335026
[5,] 0.6001646 1.5009145
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.3712317
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.3712317
[2,] 0.2797962
>
>
>
> 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] [,7]
row3 -0.14234095 -1.6039206 0.169875 0.53579 -0.4477732 0.9319960 -0.3449282
row1 0.04801073 -0.6084431 -1.244094 -1.08033 0.6046920 -0.2776777 -1.8496205
[,8] [,9] [,10] [,11] [,12] [,13]
row3 -0.3099385 -0.99494961 1.3890662 0.8161846 0.6369375 -0.6794703
row1 -0.3781968 -0.06447619 -0.8546881 1.2280529 -0.9253382 -2.3801591
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 0.8402945 -0.2505784 0.1597793 -1.9004195 0.1722902 1.9957175 0.2154881
row1 -0.6383354 -0.6611162 1.2350034 0.9341827 0.2252876 -0.2889196 1.6919516
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -1.24793 -0.04379206 -0.9262503 1.49331 -0.8179079 1.61603 0.0532483
[,8] [,9] [,10]
row2 -1.536584 -0.3817394 -0.2331654
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.1675864 0.3267241 0.6206062 -1.118017 0.5514612 -0.6544769 0.1099508
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.5398518 -2.491217 0.5317679 1.17893 -0.2737777 -0.1401561 0.2373613
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -1.175047 0.06392717 1.804218 -0.5613185 -1.811452 0.05843792
>
>
> 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: 0x618961d8dca0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3694ed150b5114"
[2] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3694ed1e2095af"
[3] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3694ed1ffec580"
[4] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3694ed51ad7f14"
[5] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3694ed44f3cf97"
[6] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3694ed6dd20654"
[7] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3694ed230cae27"
[8] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3694ed45103dec"
[9] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3694eda7bcd92"
[10] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3694ed580771da"
[11] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3694ed4d4659ac"
[12] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3694ed2ca99eb0"
[13] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3694ed311b454d"
[14] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3694ed3248190f"
[15] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM3694ed5892f912"
>
>
> ### 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: 0x61896206afe0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x61896206afe0>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x61896206afe0>
> rowMedians(tmp)
[1] -0.141916737 0.413924298 -0.389761128 -0.444671822 0.876238142
[6] -0.274095290 -0.306077746 0.291821161 -0.116804378 -0.198327979
[11] -0.344549329 0.260670056 -0.026338893 -0.114355859 -0.027449996
[16] 0.068209421 0.475043273 -0.282442536 -0.100689903 0.066807118
[21] 0.242252948 -0.372234285 0.056982557 -0.053267217 0.368861120
[26] 0.425084129 -0.116004153 -0.175246714 0.087966649 -0.136300493
[31] 0.293408274 0.041430923 0.676789071 0.520668437 -0.236746272
[36] -0.741379071 0.378916190 0.435469207 -0.059896169 0.058798854
[41] -0.098688558 0.031324437 0.074016346 0.767997930 -0.138948558
[46] 0.211993347 -0.020497295 -0.049596524 -0.104745483 -0.002752440
[51] 0.256258643 -0.069605724 -0.070949852 0.480086289 -0.087988533
[56] -0.278083460 0.385471414 0.332471252 -0.451785278 -0.927608666
[61] 0.543840262 0.121452417 0.230373612 0.048911647 -0.572414733
[66] 0.152095755 0.418865433 0.062546589 -0.071384335 0.548995792
[71] 0.371227647 0.037281245 0.290562800 0.122764946 -0.201184890
[76] 0.103979506 0.073512359 0.095638212 -0.349406325 -0.262151566
[81] -0.322108644 -0.058885933 1.156871997 -0.094860398 -0.399008013
[86] 0.767242339 0.828999160 -0.152434773 0.407577913 0.419452369
[91] -0.192963670 0.265379851 0.028960866 0.118415536 0.310037056
[96] 0.261621157 0.353100484 0.380119550 0.237406266 -0.501752662
[101] -0.510637942 0.261658128 -0.189144554 -0.031126126 -0.386183567
[106] 0.237485106 -0.547499550 -0.105706548 -0.041686156 -0.324660752
[111] 0.338943228 0.294560418 -0.881127500 -0.033161543 0.276714001
[116] 0.120268590 0.122397242 -0.125069552 -0.028520781 -0.072978457
[121] -0.393822850 0.516291473 0.004310044 -0.114671632 -0.737421123
[126] -0.319469706 0.112471771 -0.181054632 -0.134097959 -0.396620860
[131] -0.334004762 0.123085611 -0.083736334 0.683832002 0.130511393
[136] 0.240430577 0.069137812 -0.117130994 -0.559370749 -0.270395180
[141] -0.639305606 0.193891564 -0.010985836 -0.040420527 -0.263917444
[146] 0.423187901 0.281803056 0.428385501 -0.223010302 0.241554296
[151] -0.625384795 -0.051478466 0.118622042 0.055548067 -0.151735847
[156] 0.094256575 0.211515636 -0.042573175 -0.552896409 -0.013933163
[161] -0.246336229 0.184889302 0.357792340 0.148563139 0.275866142
[166] -0.107847663 0.314696327 -0.221314607 -0.131716581 -0.363552310
[171] 0.194058759 -0.134018156 -0.275969519 0.412598853 0.301580214
[176] 0.083403930 0.132955655 0.563808969 0.102829572 -0.561348811
[181] -0.472519016 -0.015943504 0.303633803 -0.380676769 -0.059615106
[186] -0.167925737 0.490202106 0.224308182 0.154261879 -0.110787636
[191] -0.186399486 0.340669856 0.001640992 -0.123253425 -0.098717177
[196] -0.101763164 0.144196505 -0.268077346 -0.308914430 0.605318486
[201] 0.067744504 -0.054684365 -0.484750950 0.143263004 0.188301904
[206] -0.158679937 -0.168375192 0.020180945 -0.604600776 -0.061599428
[211] -0.048253957 -0.716526253 0.275926590 0.078593938 -0.067858903
[216] 0.209902585 -0.162037056 -0.543637500 0.258980706 -0.004988111
[221] -0.027407014 -0.187878058 -0.135886342 0.810416818 -0.177471953
[226] -0.371603380 -0.332755217 -0.282592665 -0.022909023 -0.255449869
>
> proc.time()
user system elapsed
1.261 0.693 1.941
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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: 0x588641107370>
> .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: 0x588641107370>
> .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: 0x588641107370>
> .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: 0x588641107370>
> 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: 0x5886410ef1c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5886410ef1c0>
> .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: 0x5886410ef1c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5886410ef1c0>
> .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: 0x5886410ef1c0>
> 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: 0x5886413d2120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5886413d2120>
> .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: 0x5886413d2120>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5886413d2120>
> .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: 0x5886413d2120>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x5886413d2120>
> .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: 0x5886413d2120>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x5886413d2120>
> .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: 0x5886413d2120>
> 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: 0x588640122390>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x588640122390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x588640122390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x588640122390>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile3695ce34a938c1" "BufferedMatrixFile3695ce6ad35ee3"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile3695ce34a938c1" "BufferedMatrixFile3695ce6ad35ee3"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5886400193d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5886400193d0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5886400193d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5886400193d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x5886400193d0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x5886400193d0>
> .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: 0x588641b4efa0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x588641b4efa0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x588641b4efa0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x588641b4efa0>
> 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: 0x588640326ff0>
> .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: 0x588640326ff0>
> rm(P)
>
> proc.time()
user system elapsed
0.253 0.053 0.293
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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
0.251 0.037 0.276