Ben Bolstad
| Snapshot Date: 2026-02-02 13:45 -0500 (Mon, 02 Feb 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 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-05 11:57 -0500 (Thu, 05 Feb 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" | 4888 |
| 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: 2026-02-03 21:28:13 -0500 (Tue, 03 Feb 2026) |
| EndedAt: 2026-02-03 21:28:37 -0500 (Tue, 03 Feb 2026) |
| EllapsedTime: 24.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
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### 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
###
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* 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 24.04.3 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) 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
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###
### 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) 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
0.243 0.041 0.273
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 Feb 3 21:28:28 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 Feb 3 21:28:28 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: 0x582cda6393f0>
>
>
>
> 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 Feb 3 21:28:29 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 Feb 3 21:28:29 2026"
>
> ColMode(tmp2)
<pointer: 0x582cda6393f0>
>
>
>
> ### 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,] 97.9938729 1.0104072 0.8194684 0.8630206
[2,] -0.1275642 -0.8313647 0.1011766 1.1203895
[3,] 0.4575111 -0.2418034 0.3687130 1.1484356
[4,] -1.3959713 0.2572355 0.1535377 0.3795355
> 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,] 97.9938729 1.0104072 0.8194684 0.8630206
[2,] 0.1275642 0.8313647 0.1011766 1.1203895
[3,] 0.4575111 0.2418034 0.3687130 1.1484356
[4,] 1.3959713 0.2572355 0.1535377 0.3795355
> 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,] 9.8991855 1.0051902 0.9052450 0.9289890
[2,] 0.3571613 0.9117920 0.3180828 1.0584845
[3,] 0.6763957 0.4917350 0.6072175 1.0716509
[4,] 1.1815123 0.5071839 0.3918389 0.6160645
>
> 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,] 221.98573 36.06231 34.87192 35.15291
[2,] 28.69918 34.94929 28.28200 36.70523
[3,] 32.22147 30.15915 31.44089 36.86494
[4,] 38.21109 30.32907 29.07193 31.54018
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x582cdb635a30>
> exp(tmp5)
<pointer: 0x582cdb635a30>
> log(tmp5,2)
<pointer: 0x582cdb635a30>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 462.0342
> Min(tmp5)
[1] 52.90287
> mean(tmp5)
[1] 72.89788
> Sum(tmp5)
[1] 14579.58
> Var(tmp5)
[1] 835.4384
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 94.86125 69.91915 69.71815 72.31898 67.25118 69.35258 71.96614 70.75305
[9] 71.08794 71.75036
> rowSums(tmp5)
[1] 1897.225 1398.383 1394.363 1446.380 1345.024 1387.052 1439.323 1415.061
[9] 1421.759 1435.007
> rowVars(tmp5)
[1] 7544.97486 79.76126 56.82458 69.84917 65.40783 51.81098
[7] 103.40275 58.30024 74.02457 60.26286
> rowSd(tmp5)
[1] 86.861815 8.930916 7.538208 8.357582 8.087511 7.197985 10.168714
[8] 7.635460 8.603754 7.762916
> rowMax(tmp5)
[1] 462.03421 85.07178 89.52156 88.87462 82.88535 86.07828 91.26941
[8] 87.91710 89.18024 84.37893
> rowMin(tmp5)
[1] 57.54953 55.04417 58.68063 58.24079 52.90287 57.73975 55.23807 56.61259
[9] 58.43600 58.47754
>
> colMeans(tmp5)
[1] 109.99281 69.69496 68.39695 71.65441 74.62080 72.41322 66.81466
[8] 69.86632 68.13493 70.22940 73.82335 70.82086 71.71823 72.20445
[15] 74.40888 72.90468 66.72706 72.54104 70.01965 70.97095
> colSums(tmp5)
[1] 1099.9281 696.9496 683.9695 716.5441 746.2080 724.1322 668.1466
[8] 698.6632 681.3493 702.2940 738.2335 708.2086 717.1823 722.0445
[15] 744.0888 729.0468 667.2706 725.4104 700.1965 709.7095
> colVars(tmp5)
[1] 15403.55854 88.76233 79.14993 67.28308 103.81143 29.48575
[7] 61.01743 21.88023 61.36413 74.58567 72.88886 103.75029
[13] 94.65131 131.45423 85.24918 44.17406 70.23292 32.58554
[19] 61.56559 66.31780
> colSd(tmp5)
[1] 124.111073 9.421376 8.896625 8.202626 10.188790 5.430079
[7] 7.811365 4.677631 7.833526 8.636299 8.537497 10.185789
[13] 9.728891 11.465349 9.233048 6.646357 8.380509 5.708375
[19] 7.846374 8.143574
> colMax(tmp5)
[1] 462.03421 88.67063 87.55129 83.27171 89.52156 84.44305 80.84635
[8] 79.74047 84.40389 86.15931 88.87462 89.18024 91.26941 87.91710
[15] 94.19511 82.40284 78.90839 82.03562 82.88535 84.13355
> colMin(tmp5)
[1] 57.73975 60.63146 58.86529 59.29845 55.23807 63.39436 58.75165 65.77378
[9] 57.99334 58.43600 61.68872 55.04417 61.35474 52.90287 57.74369 62.43645
[17] 56.61259 61.60943 58.68063 60.85587
>
>
> ### 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] 94.86125 69.91915 69.71815 72.31898 67.25118 NA 71.96614 70.75305
[9] 71.08794 71.75036
> rowSums(tmp5)
[1] 1897.225 1398.383 1394.363 1446.380 1345.024 NA 1439.323 1415.061
[9] 1421.759 1435.007
> rowVars(tmp5)
[1] 7544.97486 79.76126 56.82458 69.84917 65.40783 53.62198
[7] 103.40275 58.30024 74.02457 60.26286
> rowSd(tmp5)
[1] 86.861815 8.930916 7.538208 8.357582 8.087511 7.322703 10.168714
[8] 7.635460 8.603754 7.762916
> rowMax(tmp5)
[1] 462.03421 85.07178 89.52156 88.87462 82.88535 NA 91.26941
[8] 87.91710 89.18024 84.37893
> rowMin(tmp5)
[1] 57.54953 55.04417 58.68063 58.24079 52.90287 NA 55.23807 56.61259
[9] 58.43600 58.47754
>
> colMeans(tmp5)
[1] 109.99281 NA 68.39695 71.65441 74.62080 72.41322 66.81466
[8] 69.86632 68.13493 70.22940 73.82335 70.82086 71.71823 72.20445
[15] 74.40888 72.90468 66.72706 72.54104 70.01965 70.97095
> colSums(tmp5)
[1] 1099.9281 NA 683.9695 716.5441 746.2080 724.1322 668.1466
[8] 698.6632 681.3493 702.2940 738.2335 708.2086 717.1823 722.0445
[15] 744.0888 729.0468 667.2706 725.4104 700.1965 709.7095
> colVars(tmp5)
[1] 15403.55854 NA 79.14993 67.28308 103.81143 29.48575
[7] 61.01743 21.88023 61.36413 74.58567 72.88886 103.75029
[13] 94.65131 131.45423 85.24918 44.17406 70.23292 32.58554
[19] 61.56559 66.31780
> colSd(tmp5)
[1] 124.111073 NA 8.896625 8.202626 10.188790 5.430079
[7] 7.811365 4.677631 7.833526 8.636299 8.537497 10.185789
[13] 9.728891 11.465349 9.233048 6.646357 8.380509 5.708375
[19] 7.846374 8.143574
> colMax(tmp5)
[1] 462.03421 NA 87.55129 83.27171 89.52156 84.44305 80.84635
[8] 79.74047 84.40389 86.15931 88.87462 89.18024 91.26941 87.91710
[15] 94.19511 82.40284 78.90839 82.03562 82.88535 84.13355
> colMin(tmp5)
[1] 57.73975 NA 58.86529 59.29845 55.23807 63.39436 58.75165 65.77378
[9] 57.99334 58.43600 61.68872 55.04417 61.35474 52.90287 57.74369 62.43645
[17] 56.61259 61.60943 58.68063 60.85587
>
> Max(tmp5,na.rm=TRUE)
[1] 462.0342
> Min(tmp5,na.rm=TRUE)
[1] 52.90287
> mean(tmp5,na.rm=TRUE)
[1] 72.93716
> Sum(tmp5,na.rm=TRUE)
[1] 14514.5
> Var(tmp5,na.rm=TRUE)
[1] 839.3476
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 94.86125 69.91915 69.71815 72.31898 67.25118 69.57744 71.96614 70.75305
[9] 71.08794 71.75036
> rowSums(tmp5,na.rm=TRUE)
[1] 1897.225 1398.383 1394.363 1446.380 1345.024 1321.971 1439.323 1415.061
[9] 1421.759 1435.007
> rowVars(tmp5,na.rm=TRUE)
[1] 7544.97486 79.76126 56.82458 69.84917 65.40783 53.62198
[7] 103.40275 58.30024 74.02457 60.26286
> rowSd(tmp5,na.rm=TRUE)
[1] 86.861815 8.930916 7.538208 8.357582 8.087511 7.322703 10.168714
[8] 7.635460 8.603754 7.762916
> rowMax(tmp5,na.rm=TRUE)
[1] 462.03421 85.07178 89.52156 88.87462 82.88535 86.07828 91.26941
[8] 87.91710 89.18024 84.37893
> rowMin(tmp5,na.rm=TRUE)
[1] 57.54953 55.04417 58.68063 58.24079 52.90287 57.73975 55.23807 56.61259
[9] 58.43600 58.47754
>
> colMeans(tmp5,na.rm=TRUE)
[1] 109.99281 70.20770 68.39695 71.65441 74.62080 72.41322 66.81466
[8] 69.86632 68.13493 70.22940 73.82335 70.82086 71.71823 72.20445
[15] 74.40888 72.90468 66.72706 72.54104 70.01965 70.97095
> colSums(tmp5,na.rm=TRUE)
[1] 1099.9281 631.8693 683.9695 716.5441 746.2080 724.1322 668.1466
[8] 698.6632 681.3493 702.2940 738.2335 708.2086 717.1823 722.0445
[15] 744.0888 729.0468 667.2706 725.4104 700.1965 709.7095
> colVars(tmp5,na.rm=TRUE)
[1] 15403.55854 96.89996 79.14993 67.28308 103.81143 29.48575
[7] 61.01743 21.88023 61.36413 74.58567 72.88886 103.75029
[13] 94.65131 131.45423 85.24918 44.17406 70.23292 32.58554
[19] 61.56559 66.31780
> colSd(tmp5,na.rm=TRUE)
[1] 124.111073 9.843778 8.896625 8.202626 10.188790 5.430079
[7] 7.811365 4.677631 7.833526 8.636299 8.537497 10.185789
[13] 9.728891 11.465349 9.233048 6.646357 8.380509 5.708375
[19] 7.846374 8.143574
> colMax(tmp5,na.rm=TRUE)
[1] 462.03421 88.67063 87.55129 83.27171 89.52156 84.44305 80.84635
[8] 79.74047 84.40389 86.15931 88.87462 89.18024 91.26941 87.91710
[15] 94.19511 82.40284 78.90839 82.03562 82.88535 84.13355
> colMin(tmp5,na.rm=TRUE)
[1] 57.73975 60.63146 58.86529 59.29845 55.23807 63.39436 58.75165 65.77378
[9] 57.99334 58.43600 61.68872 55.04417 61.35474 52.90287 57.74369 62.43645
[17] 56.61259 61.60943 58.68063 60.85587
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 94.86125 69.91915 69.71815 72.31898 67.25118 NaN 71.96614 70.75305
[9] 71.08794 71.75036
> rowSums(tmp5,na.rm=TRUE)
[1] 1897.225 1398.383 1394.363 1446.380 1345.024 0.000 1439.323 1415.061
[9] 1421.759 1435.007
> rowVars(tmp5,na.rm=TRUE)
[1] 7544.97486 79.76126 56.82458 69.84917 65.40783 NA
[7] 103.40275 58.30024 74.02457 60.26286
> rowSd(tmp5,na.rm=TRUE)
[1] 86.861815 8.930916 7.538208 8.357582 8.087511 NA 10.168714
[8] 7.635460 8.603754 7.762916
> rowMax(tmp5,na.rm=TRUE)
[1] 462.03421 85.07178 89.52156 88.87462 82.88535 NA 91.26941
[8] 87.91710 89.18024 84.37893
> rowMin(tmp5,na.rm=TRUE)
[1] 57.54953 55.04417 58.68063 58.24079 52.90287 NA 55.23807 56.61259
[9] 58.43600 58.47754
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 115.79870 NaN 68.48070 72.30094 74.53913 72.47990 67.70123
[8] 69.99795 66.32727 70.17496 74.85318 70.70788 71.80475 70.66291
[15] 74.45907 73.97858 67.19656 72.89693 70.43361 70.83409
> colSums(tmp5,na.rm=TRUE)
[1] 1042.1883 0.0000 616.3263 650.7085 670.8522 652.3191 609.3110
[8] 629.9815 596.9455 631.5746 673.6786 636.3709 646.2427 635.9662
[15] 670.1316 665.8072 604.7690 656.0724 633.9025 637.5068
> colVars(tmp5,na.rm=TRUE)
[1] 16949.78357 NA 88.96477 70.99088 116.71283 33.12145
[7] 59.80204 24.42034 32.27369 83.87553 70.06891 116.57549
[13] 106.39852 121.15224 95.87699 36.72175 76.53224 35.23378
[19] 67.33340 74.39681
> colSd(tmp5,na.rm=TRUE)
[1] 130.191334 NA 9.432114 8.425609 10.803371 5.755124
[7] 7.733178 4.941694 5.680993 9.158359 8.370717 10.797013
[13] 10.314966 11.006918 9.791680 6.059847 8.748270 5.935805
[19] 8.205693 8.625359
> colMax(tmp5,na.rm=TRUE)
[1] 462.03421 -Inf 87.55129 83.27171 89.52156 84.44305 80.84635
[8] 79.74047 76.56802 86.15931 88.87462 89.18024 91.26941 87.91710
[15] 94.19511 82.40284 78.90839 82.03562 82.88535 84.13355
> colMin(tmp5,na.rm=TRUE)
[1] 58.47754 Inf 58.86529 59.29845 55.23807 63.39436 58.75165 65.77378
[9] 57.99334 58.43600 61.68872 55.04417 61.35474 52.90287 57.74369 62.43645
[17] 56.61259 61.60943 58.68063 60.85587
>
>
>
>
> 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] 176.9401 135.5348 244.2530 360.9964 177.3508 246.6369 222.8772 141.0445
[9] 261.0766 319.5407
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 176.9401 135.5348 244.2530 360.9964 177.3508 246.6369 222.8772 141.0445
[9] 261.0766 319.5407
>
>
>
> 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] -5.684342e-14 -2.273737e-13 2.842171e-14 0.000000e+00 -5.684342e-14
[6] 1.136868e-13 1.705303e-13 4.263256e-14 0.000000e+00 -1.989520e-13
[11] -2.842171e-14 5.684342e-14 1.705303e-13 5.684342e-14 1.136868e-13
[16] 2.273737e-13 1.705303e-13 -5.684342e-14 -2.273737e-13 5.684342e-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)
+ }
5 1
2 1
3 5
7 1
8 6
3 2
8 8
1 7
5 11
4 6
3 14
10 4
6 19
7 2
6 4
4 19
3 8
10 18
3 16
1 6
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] 3.489019
> Min(tmp)
[1] -3.50362
> mean(tmp)
[1] -0.06303018
> Sum(tmp)
[1] -6.303018
> Var(tmp)
[1] 1.180993
>
> rowMeans(tmp)
[1] -0.06303018
> rowSums(tmp)
[1] -6.303018
> rowVars(tmp)
[1] 1.180993
> rowSd(tmp)
[1] 1.086735
> rowMax(tmp)
[1] 3.489019
> rowMin(tmp)
[1] -3.50362
>
> colMeans(tmp)
[1] -0.151363754 0.397072376 -1.986409418 0.694904509 -1.922861131
[6] -0.220922972 -3.503619673 -0.828460330 -0.383448197 0.450479523
[11] -1.178395470 -1.689965141 -1.476841014 1.779496626 -0.883093139
[16] 1.043820287 -0.816688002 -0.900176496 0.530042445 -0.156919344
[21] -1.549591238 -1.176694897 0.541928829 0.035311610 -0.956511630
[26] -0.740158007 -0.740852920 0.842291297 0.771506421 0.595729043
[31] 0.003136609 0.565127753 -0.548606342 -1.442020028 -1.245579775
[36] -1.266022340 -0.123740124 1.138586401 1.245948406 -0.821201027
[41] 0.349868376 0.015662163 1.195519015 -0.508697117 -0.116436929
[46] 0.058041840 0.967797138 0.101485273 -0.283970157 -0.080236906
[51] 0.395140655 -0.132682821 -0.045086853 1.237328983 -0.379243384
[56] 1.176844940 -1.647856915 -1.082208249 3.489018682 -0.224710405
[61] -0.104537665 -0.617607306 2.334935709 -0.278047186 0.284724897
[66] 0.371045743 -0.305421829 -1.059127966 -1.018115363 1.739793210
[71] -0.494966975 -0.377951027 -0.076920191 2.289518218 1.893298220
[76] -0.767003030 -0.564421436 0.282280033 0.267461740 -0.039767339
[81] -0.055441421 1.521785929 -0.258473891 0.458951814 0.761968768
[86] -0.762941786 1.268714362 -2.180158962 0.056929835 -0.360638281
[91] -0.875184988 1.239748346 -0.600513436 -0.154802374 0.091183230
[96] 1.622274576 1.990045571 -0.558735099 -1.051850090 -0.625867413
> colSums(tmp)
[1] -0.151363754 0.397072376 -1.986409418 0.694904509 -1.922861131
[6] -0.220922972 -3.503619673 -0.828460330 -0.383448197 0.450479523
[11] -1.178395470 -1.689965141 -1.476841014 1.779496626 -0.883093139
[16] 1.043820287 -0.816688002 -0.900176496 0.530042445 -0.156919344
[21] -1.549591238 -1.176694897 0.541928829 0.035311610 -0.956511630
[26] -0.740158007 -0.740852920 0.842291297 0.771506421 0.595729043
[31] 0.003136609 0.565127753 -0.548606342 -1.442020028 -1.245579775
[36] -1.266022340 -0.123740124 1.138586401 1.245948406 -0.821201027
[41] 0.349868376 0.015662163 1.195519015 -0.508697117 -0.116436929
[46] 0.058041840 0.967797138 0.101485273 -0.283970157 -0.080236906
[51] 0.395140655 -0.132682821 -0.045086853 1.237328983 -0.379243384
[56] 1.176844940 -1.647856915 -1.082208249 3.489018682 -0.224710405
[61] -0.104537665 -0.617607306 2.334935709 -0.278047186 0.284724897
[66] 0.371045743 -0.305421829 -1.059127966 -1.018115363 1.739793210
[71] -0.494966975 -0.377951027 -0.076920191 2.289518218 1.893298220
[76] -0.767003030 -0.564421436 0.282280033 0.267461740 -0.039767339
[81] -0.055441421 1.521785929 -0.258473891 0.458951814 0.761968768
[86] -0.762941786 1.268714362 -2.180158962 0.056929835 -0.360638281
[91] -0.875184988 1.239748346 -0.600513436 -0.154802374 0.091183230
[96] 1.622274576 1.990045571 -0.558735099 -1.051850090 -0.625867413
> 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] -0.151363754 0.397072376 -1.986409418 0.694904509 -1.922861131
[6] -0.220922972 -3.503619673 -0.828460330 -0.383448197 0.450479523
[11] -1.178395470 -1.689965141 -1.476841014 1.779496626 -0.883093139
[16] 1.043820287 -0.816688002 -0.900176496 0.530042445 -0.156919344
[21] -1.549591238 -1.176694897 0.541928829 0.035311610 -0.956511630
[26] -0.740158007 -0.740852920 0.842291297 0.771506421 0.595729043
[31] 0.003136609 0.565127753 -0.548606342 -1.442020028 -1.245579775
[36] -1.266022340 -0.123740124 1.138586401 1.245948406 -0.821201027
[41] 0.349868376 0.015662163 1.195519015 -0.508697117 -0.116436929
[46] 0.058041840 0.967797138 0.101485273 -0.283970157 -0.080236906
[51] 0.395140655 -0.132682821 -0.045086853 1.237328983 -0.379243384
[56] 1.176844940 -1.647856915 -1.082208249 3.489018682 -0.224710405
[61] -0.104537665 -0.617607306 2.334935709 -0.278047186 0.284724897
[66] 0.371045743 -0.305421829 -1.059127966 -1.018115363 1.739793210
[71] -0.494966975 -0.377951027 -0.076920191 2.289518218 1.893298220
[76] -0.767003030 -0.564421436 0.282280033 0.267461740 -0.039767339
[81] -0.055441421 1.521785929 -0.258473891 0.458951814 0.761968768
[86] -0.762941786 1.268714362 -2.180158962 0.056929835 -0.360638281
[91] -0.875184988 1.239748346 -0.600513436 -0.154802374 0.091183230
[96] 1.622274576 1.990045571 -0.558735099 -1.051850090 -0.625867413
> colMin(tmp)
[1] -0.151363754 0.397072376 -1.986409418 0.694904509 -1.922861131
[6] -0.220922972 -3.503619673 -0.828460330 -0.383448197 0.450479523
[11] -1.178395470 -1.689965141 -1.476841014 1.779496626 -0.883093139
[16] 1.043820287 -0.816688002 -0.900176496 0.530042445 -0.156919344
[21] -1.549591238 -1.176694897 0.541928829 0.035311610 -0.956511630
[26] -0.740158007 -0.740852920 0.842291297 0.771506421 0.595729043
[31] 0.003136609 0.565127753 -0.548606342 -1.442020028 -1.245579775
[36] -1.266022340 -0.123740124 1.138586401 1.245948406 -0.821201027
[41] 0.349868376 0.015662163 1.195519015 -0.508697117 -0.116436929
[46] 0.058041840 0.967797138 0.101485273 -0.283970157 -0.080236906
[51] 0.395140655 -0.132682821 -0.045086853 1.237328983 -0.379243384
[56] 1.176844940 -1.647856915 -1.082208249 3.489018682 -0.224710405
[61] -0.104537665 -0.617607306 2.334935709 -0.278047186 0.284724897
[66] 0.371045743 -0.305421829 -1.059127966 -1.018115363 1.739793210
[71] -0.494966975 -0.377951027 -0.076920191 2.289518218 1.893298220
[76] -0.767003030 -0.564421436 0.282280033 0.267461740 -0.039767339
[81] -0.055441421 1.521785929 -0.258473891 0.458951814 0.761968768
[86] -0.762941786 1.268714362 -2.180158962 0.056929835 -0.360638281
[91] -0.875184988 1.239748346 -0.600513436 -0.154802374 0.091183230
[96] 1.622274576 1.990045571 -0.558735099 -1.051850090 -0.625867413
> colMedians(tmp)
[1] -0.151363754 0.397072376 -1.986409418 0.694904509 -1.922861131
[6] -0.220922972 -3.503619673 -0.828460330 -0.383448197 0.450479523
[11] -1.178395470 -1.689965141 -1.476841014 1.779496626 -0.883093139
[16] 1.043820287 -0.816688002 -0.900176496 0.530042445 -0.156919344
[21] -1.549591238 -1.176694897 0.541928829 0.035311610 -0.956511630
[26] -0.740158007 -0.740852920 0.842291297 0.771506421 0.595729043
[31] 0.003136609 0.565127753 -0.548606342 -1.442020028 -1.245579775
[36] -1.266022340 -0.123740124 1.138586401 1.245948406 -0.821201027
[41] 0.349868376 0.015662163 1.195519015 -0.508697117 -0.116436929
[46] 0.058041840 0.967797138 0.101485273 -0.283970157 -0.080236906
[51] 0.395140655 -0.132682821 -0.045086853 1.237328983 -0.379243384
[56] 1.176844940 -1.647856915 -1.082208249 3.489018682 -0.224710405
[61] -0.104537665 -0.617607306 2.334935709 -0.278047186 0.284724897
[66] 0.371045743 -0.305421829 -1.059127966 -1.018115363 1.739793210
[71] -0.494966975 -0.377951027 -0.076920191 2.289518218 1.893298220
[76] -0.767003030 -0.564421436 0.282280033 0.267461740 -0.039767339
[81] -0.055441421 1.521785929 -0.258473891 0.458951814 0.761968768
[86] -0.762941786 1.268714362 -2.180158962 0.056929835 -0.360638281
[91] -0.875184988 1.239748346 -0.600513436 -0.154802374 0.091183230
[96] 1.622274576 1.990045571 -0.558735099 -1.051850090 -0.625867413
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.1513638 0.3970724 -1.986409 0.6949045 -1.922861 -0.220923 -3.50362
[2,] -0.1513638 0.3970724 -1.986409 0.6949045 -1.922861 -0.220923 -3.50362
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.8284603 -0.3834482 0.4504795 -1.178395 -1.689965 -1.476841 1.779497
[2,] -0.8284603 -0.3834482 0.4504795 -1.178395 -1.689965 -1.476841 1.779497
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.8830931 1.04382 -0.816688 -0.9001765 0.5300424 -0.1569193 -1.549591
[2,] -0.8830931 1.04382 -0.816688 -0.9001765 0.5300424 -0.1569193 -1.549591
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -1.176695 0.5419288 0.03531161 -0.9565116 -0.740158 -0.7408529 0.8422913
[2,] -1.176695 0.5419288 0.03531161 -0.9565116 -0.740158 -0.7408529 0.8422913
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.7715064 0.595729 0.003136609 0.5651278 -0.5486063 -1.44202 -1.24558
[2,] 0.7715064 0.595729 0.003136609 0.5651278 -0.5486063 -1.44202 -1.24558
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -1.266022 -0.1237401 1.138586 1.245948 -0.821201 0.3498684 0.01566216
[2,] -1.266022 -0.1237401 1.138586 1.245948 -0.821201 0.3498684 0.01566216
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 1.195519 -0.5086971 -0.1164369 0.05804184 0.9677971 0.1014853 -0.2839702
[2,] 1.195519 -0.5086971 -0.1164369 0.05804184 0.9677971 0.1014853 -0.2839702
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -0.08023691 0.3951407 -0.1326828 -0.04508685 1.237329 -0.3792434 1.176845
[2,] -0.08023691 0.3951407 -0.1326828 -0.04508685 1.237329 -0.3792434 1.176845
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -1.647857 -1.082208 3.489019 -0.2247104 -0.1045377 -0.6176073 2.334936
[2,] -1.647857 -1.082208 3.489019 -0.2247104 -0.1045377 -0.6176073 2.334936
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -0.2780472 0.2847249 0.3710457 -0.3054218 -1.059128 -1.018115 1.739793
[2,] -0.2780472 0.2847249 0.3710457 -0.3054218 -1.059128 -1.018115 1.739793
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] -0.494967 -0.377951 -0.07692019 2.289518 1.893298 -0.767003 -0.5644214
[2,] -0.494967 -0.377951 -0.07692019 2.289518 1.893298 -0.767003 -0.5644214
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.28228 0.2674617 -0.03976734 -0.05544142 1.521786 -0.2584739 0.4589518
[2,] 0.28228 0.2674617 -0.03976734 -0.05544142 1.521786 -0.2584739 0.4589518
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.7619688 -0.7629418 1.268714 -2.180159 0.05692984 -0.3606383 -0.875185
[2,] 0.7619688 -0.7629418 1.268714 -2.180159 0.05692984 -0.3606383 -0.875185
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 1.239748 -0.6005134 -0.1548024 0.09118323 1.622275 1.990046 -0.5587351
[2,] 1.239748 -0.6005134 -0.1548024 0.09118323 1.622275 1.990046 -0.5587351
[,99] [,100]
[1,] -1.05185 -0.6258674
[2,] -1.05185 -0.6258674
>
>
> Max(tmp2)
[1] 2.293209
> Min(tmp2)
[1] -2.712897
> mean(tmp2)
[1] -0.09435708
> Sum(tmp2)
[1] -9.435708
> Var(tmp2)
[1] 1.042474
>
> rowMeans(tmp2)
[1] -0.56522109 -0.49195764 1.02991525 -0.70849254 -0.67136119 0.41581748
[7] 0.53165212 1.35062530 0.74186165 0.09211541 1.33018381 -0.91436042
[13] 1.07385498 2.29320901 0.06348128 1.75977928 -0.60973723 -1.44849266
[19] -1.98479859 1.27752316 -0.71512134 0.69537453 -0.75891597 0.14812889
[25] 0.40834650 1.32758010 -1.50903265 -1.07859180 -1.75454314 -0.64909747
[31] -0.86258936 1.30436605 0.80180377 0.28132465 1.28661426 0.96975749
[37] -0.39606438 0.38380288 -0.44228330 0.29932491 -0.22400771 0.56240887
[43] 0.50287796 -2.71289737 -0.03257649 0.25280111 -1.30304789 -0.60273834
[49] 1.60016734 0.30833838 -1.37216065 1.06678002 -0.49610873 -0.47792531
[55] 0.92895822 -0.42785891 0.29272735 1.15681897 -1.47826951 0.53886046
[61] 1.79806391 -0.79055570 -1.03637262 -0.07340417 -0.45229367 -1.31588109
[67] -0.25994680 0.58348761 0.49562609 -0.98544233 -0.56573453 0.37509553
[73] -1.15544388 -0.92254930 -1.08212624 -1.14390270 -1.12715608 -1.47396674
[79] -1.88905382 0.52196566 -0.94281658 -1.18395828 -1.02298218 0.76747743
[85] 0.15489490 1.73459323 0.49669450 -0.88681160 0.75370622 -0.20322475
[91] -0.57799812 -1.24982483 -0.42892316 0.94007932 -1.39961820 0.26744857
[97] -0.03121120 1.68254927 1.15733926 -1.35246039
> rowSums(tmp2)
[1] -0.56522109 -0.49195764 1.02991525 -0.70849254 -0.67136119 0.41581748
[7] 0.53165212 1.35062530 0.74186165 0.09211541 1.33018381 -0.91436042
[13] 1.07385498 2.29320901 0.06348128 1.75977928 -0.60973723 -1.44849266
[19] -1.98479859 1.27752316 -0.71512134 0.69537453 -0.75891597 0.14812889
[25] 0.40834650 1.32758010 -1.50903265 -1.07859180 -1.75454314 -0.64909747
[31] -0.86258936 1.30436605 0.80180377 0.28132465 1.28661426 0.96975749
[37] -0.39606438 0.38380288 -0.44228330 0.29932491 -0.22400771 0.56240887
[43] 0.50287796 -2.71289737 -0.03257649 0.25280111 -1.30304789 -0.60273834
[49] 1.60016734 0.30833838 -1.37216065 1.06678002 -0.49610873 -0.47792531
[55] 0.92895822 -0.42785891 0.29272735 1.15681897 -1.47826951 0.53886046
[61] 1.79806391 -0.79055570 -1.03637262 -0.07340417 -0.45229367 -1.31588109
[67] -0.25994680 0.58348761 0.49562609 -0.98544233 -0.56573453 0.37509553
[73] -1.15544388 -0.92254930 -1.08212624 -1.14390270 -1.12715608 -1.47396674
[79] -1.88905382 0.52196566 -0.94281658 -1.18395828 -1.02298218 0.76747743
[85] 0.15489490 1.73459323 0.49669450 -0.88681160 0.75370622 -0.20322475
[91] -0.57799812 -1.24982483 -0.42892316 0.94007932 -1.39961820 0.26744857
[97] -0.03121120 1.68254927 1.15733926 -1.35246039
> 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] -0.56522109 -0.49195764 1.02991525 -0.70849254 -0.67136119 0.41581748
[7] 0.53165212 1.35062530 0.74186165 0.09211541 1.33018381 -0.91436042
[13] 1.07385498 2.29320901 0.06348128 1.75977928 -0.60973723 -1.44849266
[19] -1.98479859 1.27752316 -0.71512134 0.69537453 -0.75891597 0.14812889
[25] 0.40834650 1.32758010 -1.50903265 -1.07859180 -1.75454314 -0.64909747
[31] -0.86258936 1.30436605 0.80180377 0.28132465 1.28661426 0.96975749
[37] -0.39606438 0.38380288 -0.44228330 0.29932491 -0.22400771 0.56240887
[43] 0.50287796 -2.71289737 -0.03257649 0.25280111 -1.30304789 -0.60273834
[49] 1.60016734 0.30833838 -1.37216065 1.06678002 -0.49610873 -0.47792531
[55] 0.92895822 -0.42785891 0.29272735 1.15681897 -1.47826951 0.53886046
[61] 1.79806391 -0.79055570 -1.03637262 -0.07340417 -0.45229367 -1.31588109
[67] -0.25994680 0.58348761 0.49562609 -0.98544233 -0.56573453 0.37509553
[73] -1.15544388 -0.92254930 -1.08212624 -1.14390270 -1.12715608 -1.47396674
[79] -1.88905382 0.52196566 -0.94281658 -1.18395828 -1.02298218 0.76747743
[85] 0.15489490 1.73459323 0.49669450 -0.88681160 0.75370622 -0.20322475
[91] -0.57799812 -1.24982483 -0.42892316 0.94007932 -1.39961820 0.26744857
[97] -0.03121120 1.68254927 1.15733926 -1.35246039
> rowMin(tmp2)
[1] -0.56522109 -0.49195764 1.02991525 -0.70849254 -0.67136119 0.41581748
[7] 0.53165212 1.35062530 0.74186165 0.09211541 1.33018381 -0.91436042
[13] 1.07385498 2.29320901 0.06348128 1.75977928 -0.60973723 -1.44849266
[19] -1.98479859 1.27752316 -0.71512134 0.69537453 -0.75891597 0.14812889
[25] 0.40834650 1.32758010 -1.50903265 -1.07859180 -1.75454314 -0.64909747
[31] -0.86258936 1.30436605 0.80180377 0.28132465 1.28661426 0.96975749
[37] -0.39606438 0.38380288 -0.44228330 0.29932491 -0.22400771 0.56240887
[43] 0.50287796 -2.71289737 -0.03257649 0.25280111 -1.30304789 -0.60273834
[49] 1.60016734 0.30833838 -1.37216065 1.06678002 -0.49610873 -0.47792531
[55] 0.92895822 -0.42785891 0.29272735 1.15681897 -1.47826951 0.53886046
[61] 1.79806391 -0.79055570 -1.03637262 -0.07340417 -0.45229367 -1.31588109
[67] -0.25994680 0.58348761 0.49562609 -0.98544233 -0.56573453 0.37509553
[73] -1.15544388 -0.92254930 -1.08212624 -1.14390270 -1.12715608 -1.47396674
[79] -1.88905382 0.52196566 -0.94281658 -1.18395828 -1.02298218 0.76747743
[85] 0.15489490 1.73459323 0.49669450 -0.88681160 0.75370622 -0.20322475
[91] -0.57799812 -1.24982483 -0.42892316 0.94007932 -1.39961820 0.26744857
[97] -0.03121120 1.68254927 1.15733926 -1.35246039
>
> colMeans(tmp2)
[1] -0.09435708
> colSums(tmp2)
[1] -9.435708
> colVars(tmp2)
[1] 1.042474
> colSd(tmp2)
[1] 1.021016
> colMax(tmp2)
[1] 2.293209
> colMin(tmp2)
[1] -2.712897
> colMedians(tmp2)
[1] -0.1383145
> colRanges(tmp2)
[,1]
[1,] -2.712897
[2,] 2.293209
>
> 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] 0.3685318 -1.1236556 0.8066486 12.4997527 3.8333460 4.0699344
[7] 0.3351187 -0.1481244 4.1140178 -2.9658505
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.3184356
[2,] -0.3599023
[3,] 0.1680886
[4,] 0.5122540
[5,] 1.4059498
>
> rowApply(tmp,sum)
[1] -2.537864 1.571260 3.714678 1.475250 4.623225 3.725655 6.840542
[8] -4.399503 5.358709 1.417768
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 9 4 7 6 2 2 4 7 8 1
[2,] 4 8 1 2 7 9 3 1 3 6
[3,] 7 2 8 3 8 3 8 5 4 5
[4,] 6 5 10 9 10 10 7 9 10 4
[5,] 3 3 3 5 9 8 6 10 7 2
[6,] 8 9 5 7 1 5 9 6 5 9
[7,] 1 7 6 10 4 7 1 4 2 3
[8,] 5 6 2 8 5 4 5 3 6 7
[9,] 10 1 4 1 6 6 10 8 9 10
[10,] 2 10 9 4 3 1 2 2 1 8
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 3.19271339 0.51080914 -1.57424121 -0.69933535 0.50477490 -0.53463720
[7] 1.47797807 1.52289353 0.83671900 0.36251202 -0.35626582 -2.73202853
[13] -0.07073027 1.41526966 -0.56531727 -0.36122546 0.11848569 -1.22576255
[19] 0.70006083 1.85358377
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.3954648
[2,] 0.6383417
[3,] 0.6992574
[4,] 1.1052903
[5,] 1.1452888
>
> rowApply(tmp,sum)
[1] -3.6855449 0.6428498 1.3214265 1.1927104 4.9048146
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 10 19 17 18 14
[2,] 16 8 14 17 4
[3,] 19 4 4 12 2
[4,] 13 3 20 11 1
[5,] 4 2 10 20 10
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.3954648 0.2040478 1.35420760 -0.08681086 -0.855957431 -0.7363996
[2,] 1.1452888 0.0174480 -0.92423625 -1.30699006 -1.645624354 0.6602538
[3,] 0.6992574 0.3711123 -0.69915561 2.50387682 0.006170877 -0.7463046
[4,] 1.1052903 0.9030367 0.05395084 -0.01347595 2.712116387 -0.1591197
[5,] 0.6383417 -0.9848356 -1.35900780 -1.79593530 0.288069426 0.4469329
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 1.7448946 -1.3086992 -1.0251196 -0.56847979 -0.6828696 -0.5135643
[2,] 0.2227440 1.4553947 0.3859071 0.01568736 0.4588630 -0.7233186
[3,] -0.3305907 0.9050026 -2.1754312 1.19931074 0.2423737 -0.1368010
[4,] 0.2266578 -0.1739730 0.2678779 -0.86842864 -0.2651517 -1.0955184
[5,] -0.3857276 0.6451684 3.3834848 0.58442234 -0.1094812 -0.2628262
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.00254596 -0.2924332 -0.1986845 0.48427801 -1.0430834 -0.07505746
[2,] 0.42692732 0.6410541 -0.3389136 0.08948676 0.6440035 -1.85616029
[3,] 0.36090427 0.5881547 -1.5039097 -0.02560626 0.6777949 -0.05467116
[4,] -0.28959352 -1.2751161 -0.8382079 0.14392710 -0.7794046 1.71497923
[5,] -0.57151430 1.7536102 2.3143985 -1.05331108 0.6191753 -0.95485287
[,19] [,20]
[1,] -0.732310974 1.0394160
[2,] 0.296979664 0.9780550
[3,] 0.008138234 -0.5682000
[4,] 0.305703074 -0.4828392
[5,] 0.821550829 0.8871521
>
>
> 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 : 566 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-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 -0.6748211 -0.9749948 -0.5157668 -0.410907 0.8798257 -1.891193 0.164037
col8 col9 col10 col11 col12 col13 col14
row1 0.09075949 0.4596869 0.9542089 2.058552 -1.409313 0.1644866 -2.255848
col15 col16 col17 col18 col19 col20
row1 -0.09597466 -1.467157 1.150722 1.005586 0.3177731 0.7447162
> tmp[,"col10"]
col10
row1 0.95420890
row2 -0.85948325
row3 -0.06412026
row4 -3.32083514
row5 0.25913083
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -0.6748211 -0.9749948 -0.5157668 -0.410907 0.8798257 -1.8911934 0.1640370
row5 1.1169973 -0.2164586 -1.0538474 1.463040 0.9903687 0.7260106 -0.2470562
col8 col9 col10 col11 col12 col13
row1 0.09075949 0.4596869 0.9542089 2.05855207 -1.4093127 0.1644866
row5 -1.74020230 0.2252770 0.2591308 -0.04215266 -0.4889911 -1.1631897
col14 col15 col16 col17 col18 col19
row1 -2.2558485 -0.09597466 -1.4671571 1.1507217 1.0055856 0.3177731
row5 0.1758384 -0.70267933 0.1401168 -0.5386682 0.5147072 1.1458534
col20
row1 0.7447162
row5 -1.1041437
> tmp[,c("col6","col20")]
col6 col20
row1 -1.8911934 0.74471619
row2 -1.4906929 -2.86554910
row3 0.6217329 1.04779552
row4 -0.4184642 -0.02319806
row5 0.7260106 -1.10414374
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -1.8911934 0.7447162
row5 0.7260106 -1.1041437
>
>
>
>
> 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 48.44502 49.73642 49.11928 50.06255 48.7497 105.3127 51.83364 50.85177
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.1561 51.50593 49.90812 49.9272 49.71857 48.95237 49.59702 50.60991
col17 col18 col19 col20
row1 51.18056 49.39997 50.47881 105.1829
> tmp[,"col10"]
col10
row1 51.50593
row2 30.73478
row3 29.90723
row4 30.59338
row5 49.91477
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 48.44502 49.73642 49.11928 50.06255 48.74970 105.3127 51.83364 50.85177
row5 51.45029 49.76895 51.18281 48.74577 50.40493 104.2247 50.65844 50.33878
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.15610 51.50593 49.90812 49.92720 49.71857 48.95237 49.59702 50.60991
row5 49.90892 49.91477 51.62403 49.71747 49.64585 50.30767 49.30928 49.48835
col17 col18 col19 col20
row1 51.18056 49.39997 50.47881 105.1829
row5 49.19630 48.58394 51.49590 105.9025
> tmp[,c("col6","col20")]
col6 col20
row1 105.31266 105.18291
row2 75.02539 74.15296
row3 74.26183 73.77202
row4 76.47854 75.13045
row5 104.22473 105.90245
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.3127 105.1829
row5 104.2247 105.9025
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.3127 105.1829
row5 104.2247 105.9025
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.87640908
[2,] 0.23461232
[3,] -0.01020076
[4,] -0.69762997
[5,] -0.42131975
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.25255080 2.1668371
[2,] 0.03181443 0.2467148
[3,] 1.05213376 1.1971379
[4,] 0.18875019 -0.5606209
[5,] -1.06802998 -0.2588410
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -1.6104188 0.07659118
[2,] -0.3928268 0.45588881
[3,] 0.8850570 -0.82810489
[4,] 0.3344727 0.01224836
[5,] 1.2086866 1.08660573
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -1.610419
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -1.6104188
[2,] -0.3928268
>
>
>
> 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 -0.2182037 1.79604376 -1.2244660 -0.5535552 0.6590360 0.8099225
row1 0.4689165 -0.07050049 0.9468626 0.7307964 -0.4312359 0.0928274
[,7] [,8] [,9] [,10] [,11] [,12]
row3 -1.4082446 1.3096812 -0.3304453 -0.29245989 0.3199367 -0.4690436
row1 0.6551141 0.6039418 0.3470956 -0.01800375 0.5419562 0.2299342
[,13] [,14] [,15] [,16] [,17] [,18]
row3 0.8123198 -0.9433522 -0.9069223 -0.4156846 0.8040020 -1.0293005
row1 -0.2889141 -0.9294960 1.7404020 -0.2091341 -0.9686447 0.1319751
[,19] [,20]
row3 0.07057849 0.7422459
row1 -1.17590581 -1.0220269
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -1.263018 -1.064354 -1.058344 1.193599 -0.8374301 0.2535082 1.421414
[,8] [,9] [,10]
row2 -0.6727919 0.1732451 -0.2398131
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.4987766 -0.693763 -0.1923034 0.02569862 0.4311585 0.3033033 0.9383632
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 0.4476301 -0.1628188 0.2747256 -0.633121 -1.756126 0.349532 0.08516391
[,15] [,16] [,17] [,18] [,19] [,20]
row5 0.4057856 0.07490376 -0.9699371 0.8551926 -1.124513 0.7462217
>
>
> 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: 0x582cd96789a0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2b1a3968ffcb0a"
[2] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2b1a393a4925c5"
[3] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2b1a394cc4ce8c"
[4] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2b1a397018aa8e"
[5] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2b1a39d78cc64"
[6] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2b1a397dc25dfd"
[7] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2b1a39484e115a"
[8] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2b1a391553511d"
[9] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2b1a3941d14bbb"
[10] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2b1a395334ada4"
[11] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2b1a39442ae3b7"
[12] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2b1a393e0d38ff"
[13] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2b1a391bbd2601"
[14] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2b1a395b917127"
[15] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2b1a395a1d58b"
>
>
> ### 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: 0x582cdb0e4ea0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x582cdb0e4ea0>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x582cdb0e4ea0>
> rowMedians(tmp)
[1] -0.255422547 -0.964938654 0.543668209 0.164263010 -0.065594948
[6] -0.044057377 0.732622936 0.578771217 0.457171979 0.221580977
[11] -0.178639810 -0.479843684 0.364664947 -0.236380242 -0.017869210
[16] 0.296461848 0.149203935 0.214307263 0.481681969 -0.005349076
[21] -0.226192785 0.043055348 0.540987505 0.128232498 0.307286987
[26] -0.468214557 -0.554656153 -0.003364700 -0.029022460 0.063011348
[31] -0.655334734 0.027264281 -0.221317461 -0.091544957 0.140628411
[36] -0.052923262 0.023417985 0.130373397 0.373939567 -0.419220396
[41] 0.482216033 -0.064577133 0.057742172 0.072975063 -0.183749361
[46] -0.018558272 -0.212551693 0.272343579 0.136879887 -0.027545414
[51] 0.399214453 0.183640146 0.184311833 -0.585370874 -0.506242411
[56] -0.105514155 -0.657184417 -0.237104498 0.180346525 0.057853564
[61] -0.259012757 -0.332980119 -0.295550110 -0.151808904 -0.556509613
[66] 0.056191905 -0.684815018 -0.277689622 0.373316819 0.049347671
[71] -0.198920334 0.138042419 -0.156305147 0.156596712 0.624384347
[76] 0.798628433 -0.123437115 -0.330429034 0.003741677 0.288081803
[81] -0.448382900 -0.303126942 -0.619566997 0.180952400 -0.494802326
[86] -0.213292661 0.128077644 -0.308580157 0.412859010 -0.302515901
[91] -0.203943107 0.084071671 -0.292035044 0.476771251 0.140284325
[96] 0.061884867 -0.260936866 0.076169038 -0.540935109 0.334752026
[101] 0.208996970 0.055133720 -0.033466191 -0.098657167 -0.148852424
[106] 0.195000103 -0.252885084 -0.007292968 0.372904893 0.040382542
[111] 0.107766530 -0.254107939 -0.135084515 0.265170195 -0.240664435
[116] 0.442870262 -0.539121819 -0.134983153 -0.058856715 0.169836725
[121] -0.136681627 0.089648174 -0.010370883 -0.047382531 0.019286269
[126] 0.182859382 0.474702684 0.252516886 -0.053174139 0.762372780
[131] 0.052050955 -0.842075685 -0.073056387 0.115350130 0.754472089
[136] -0.448007271 0.151320600 0.494989348 0.585270717 -0.401592408
[141] 0.716339352 -0.002836796 0.137449155 -0.068186153 -0.276349186
[146] 0.164951102 0.286536336 0.197245440 -0.235839909 -0.270106290
[151] -0.143333798 -0.303422207 -0.072662861 -0.859939609 -0.134844205
[156] 0.742074017 -0.160386386 -0.172687191 -0.215972821 0.171090356
[161] -0.199051025 -0.143878404 0.202546731 0.123951211 -0.254654332
[166] 0.103240163 0.289612012 0.262608915 -0.229316659 0.049709871
[171] 0.298094786 0.428418317 0.070382306 0.171864530 0.200230075
[176] -0.315778825 0.226541328 0.309635555 -0.029502683 -0.598473083
[181] 0.092818758 -0.712706978 -0.158815234 0.154316390 -0.319748278
[186] 0.191989332 0.137613956 0.295425738 -0.377864558 0.886480573
[191] 0.400520817 0.682929228 -0.132298353 0.128758726 -0.049594635
[196] -0.628377965 0.022701840 0.073277218 -0.045206818 -0.207194773
[201] 0.208735421 0.139832647 -0.188097927 -0.417807788 -0.156318498
[206] -0.126992539 -0.135589646 0.033909679 0.077667743 0.333220193
[211] 0.020653952 0.153611363 -0.037456868 0.175308408 0.415892820
[216] -0.414311249 0.085360827 0.468147651 0.784210982 0.413837061
[221] -0.464239549 0.001763929 -0.238952463 -0.685690463 0.290494502
[226] -0.212712897 0.128270756 -0.256354273 -0.121349624 -0.251235158
>
> proc.time()
user system elapsed
1.225 0.719 1.933
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: 0x5b341e7733f0>
> .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: 0x5b341e7733f0>
> .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: 0x5b341e7733f0>
> .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: 0x5b341e7733f0>
> 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: 0x5b341e75b240>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b341e75b240>
> .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: 0x5b341e75b240>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b341e75b240>
> .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: 0x5b341e75b240>
> 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: 0x5b341ea3e1a0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b341ea3e1a0>
> .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: 0x5b341ea3e1a0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5b341ea3e1a0>
> .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: 0x5b341ea3e1a0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x5b341ea3e1a0>
> .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: 0x5b341ea3e1a0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x5b341ea3e1a0>
> .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: 0x5b341ea3e1a0>
> 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: 0x5b341d78e410>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x5b341d78e410>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b341d78e410>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b341d78e410>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile2b1c0e24303aa1" "BufferedMatrixFile2b1c0e7cc85495"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile2b1c0e24303aa1" "BufferedMatrixFile2b1c0e7cc85495"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b341d6853d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b341d6853d0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5b341d6853d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5b341d6853d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x5b341d6853d0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x5b341d6853d0>
> .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: 0x5b341f1bb020>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b341f1bb020>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5b341f1bb020>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x5b341f1bb020>
> 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: 0x5b341d993070>
> .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: 0x5b341d993070>
> rm(P)
>
> proc.time()
user system elapsed
0.238 0.043 0.271
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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Platform: x86_64-pc-linux-gnu
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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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
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> 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 0.038 0.278