Ben Bolstad
| Snapshot Date: 2026-02-27 13:45 -0500 (Fri, 27 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 2026-02-28 11:57 -0500 (Sat, 28 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" | 4891 |
| 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: 2026-02-27 21:46:39 -0500 (Fri, 27 Feb 2026) |
| EndedAt: 2026-02-27 21:47:03 -0500 (Fri, 27 Feb 2026) |
| EllapsedTime: 24.0 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
0.256 0.036 0.279
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] "Fri Feb 27 21:46:54 2026"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Fri Feb 27 21:46:54 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: 0x5a7474829370>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Fri Feb 27 21:46:55 2026"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Fri Feb 27 21:46:55 2026"
>
> ColMode(tmp2)
<pointer: 0x5a7474829370>
>
>
>
> ### 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,] 98.94646714 -2.5570710 -1.0291915 1.3402579
[2,] 0.56766265 1.1309035 0.1072498 -0.4512304
[3,] -0.92684604 -1.3679435 -0.9402112 1.2760367
[4,] 0.01885973 -0.4533707 -0.5912261 1.0755011
> 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,] 98.94646714 2.5570710 1.0291915 1.3402579
[2,] 0.56766265 1.1309035 0.1072498 0.4512304
[3,] 0.92684604 1.3679435 0.9402112 1.2760367
[4,] 0.01885973 0.4533707 0.5912261 1.0755011
> 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,] 9.9471839 1.599084 1.0144907 1.1576951
[2,] 0.7534339 1.063439 0.3274901 0.6717369
[3,] 0.9627284 1.169591 0.9696449 1.1296180
[4,] 0.1373307 0.673328 0.7689123 1.0370637
>
> 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,] 223.41831 43.54792 36.17410 37.91721
[2,] 33.10200 36.76530 28.38215 32.16860
[3,] 35.55413 38.06386 35.63666 37.57222
[4,] 26.39217 32.18665 33.28035 36.44614
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x5a74758259b0>
> exp(tmp5)
<pointer: 0x5a74758259b0>
> log(tmp5,2)
<pointer: 0x5a74758259b0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 465.0159
> Min(tmp5)
[1] 53.93735
> mean(tmp5)
[1] 72.63479
> Sum(tmp5)
[1] 14526.96
> Var(tmp5)
[1] 846.6182
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 91.74693 70.60721 69.67674 69.76400 72.37864 71.00433 70.27500 68.71429
[9] 71.53797 70.64284
> rowSums(tmp5)
[1] 1834.939 1412.144 1393.535 1395.280 1447.573 1420.087 1405.500 1374.286
[9] 1430.759 1412.857
> rowVars(tmp5)
[1] 7805.33106 67.38415 72.20997 47.85148 52.05264 68.23065
[7] 94.44699 78.73091 65.34513 78.56503
> rowSd(tmp5)
[1] 88.347785 8.208785 8.497645 6.917477 7.214752 8.260185 9.718384
[8] 8.873044 8.083633 8.863692
> rowMax(tmp5)
[1] 465.01593 86.12372 89.09827 80.55850 89.84984 85.22680 91.39037
[8] 89.07495 87.82744 88.94394
> rowMin(tmp5)
[1] 57.42254 58.97231 57.77154 54.93184 58.84999 58.66686 55.17759 56.37612
[9] 61.35022 53.93735
>
> colMeans(tmp5)
[1] 109.38904 72.78300 71.46567 74.42178 73.10344 68.01596 68.67709
[8] 73.82796 71.73673 70.25202 68.62695 68.71344 73.49943 68.37758
[15] 70.12333 71.51517 72.14498 70.11445 70.04049 65.86737
> colSums(tmp5)
[1] 1093.8904 727.8300 714.6567 744.2178 731.0344 680.1596 686.7709
[8] 738.2796 717.3673 702.5202 686.2695 687.1344 734.9943 683.7758
[15] 701.2333 715.1517 721.4498 701.1445 700.4049 658.6737
> colVars(tmp5)
[1] 15678.29164 94.09892 55.87015 110.12705 80.76275 34.18202
[7] 96.72936 61.83663 69.99453 64.73585 62.41108 48.95746
[13] 86.79876 46.54192 150.21864 45.79741 69.25135 32.48132
[19] 75.46982 68.91868
> colSd(tmp5)
[1] 125.212985 9.700460 7.474634 10.494144 8.986810 5.846539
[7] 9.835109 7.863627 8.366273 8.045859 7.900068 6.996961
[13] 9.316585 6.822164 12.256371 6.767378 8.321739 5.699239
[19] 8.687337 8.301728
> colMax(tmp5)
[1] 465.01593 90.63928 82.20696 89.07495 89.84984 76.73728 87.82744
[8] 86.12372 83.00201 87.74877 79.16393 81.43992 89.09827 79.50576
[15] 91.39037 83.74811 88.94394 81.29354 89.64578 77.60473
> colMin(tmp5)
[1] 54.93184 58.66686 59.07373 55.17759 62.03446 59.49681 57.42254 59.90364
[9] 57.88467 61.80609 57.77154 62.10918 59.58540 58.97231 57.97628 65.18422
[17] 62.06139 62.59684 60.23069 53.93735
>
>
> ### 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] 91.74693 70.60721 69.67674 69.76400 72.37864 71.00433 70.27500 NA
[9] 71.53797 70.64284
> rowSums(tmp5)
[1] 1834.939 1412.144 1393.535 1395.280 1447.573 1420.087 1405.500 NA
[9] 1430.759 1412.857
> rowVars(tmp5)
[1] 7805.33106 67.38415 72.20997 47.85148 52.05264 68.23065
[7] 94.44699 81.42833 65.34513 78.56503
> rowSd(tmp5)
[1] 88.347785 8.208785 8.497645 6.917477 7.214752 8.260185 9.718384
[8] 9.023765 8.083633 8.863692
> rowMax(tmp5)
[1] 465.01593 86.12372 89.09827 80.55850 89.84984 85.22680 91.39037
[8] NA 87.82744 88.94394
> rowMin(tmp5)
[1] 57.42254 58.97231 57.77154 54.93184 58.84999 58.66686 55.17759 NA
[9] 61.35022 53.93735
>
> colMeans(tmp5)
[1] 109.38904 72.78300 71.46567 74.42178 73.10344 68.01596 68.67709
[8] 73.82796 71.73673 NA 68.62695 68.71344 73.49943 68.37758
[15] 70.12333 71.51517 72.14498 70.11445 70.04049 65.86737
> colSums(tmp5)
[1] 1093.8904 727.8300 714.6567 744.2178 731.0344 680.1596 686.7709
[8] 738.2796 717.3673 NA 686.2695 687.1344 734.9943 683.7758
[15] 701.2333 715.1517 721.4498 701.1445 700.4049 658.6737
> colVars(tmp5)
[1] 15678.29164 94.09892 55.87015 110.12705 80.76275 34.18202
[7] 96.72936 61.83663 69.99453 NA 62.41108 48.95746
[13] 86.79876 46.54192 150.21864 45.79741 69.25135 32.48132
[19] 75.46982 68.91868
> colSd(tmp5)
[1] 125.212985 9.700460 7.474634 10.494144 8.986810 5.846539
[7] 9.835109 7.863627 8.366273 NA 7.900068 6.996961
[13] 9.316585 6.822164 12.256371 6.767378 8.321739 5.699239
[19] 8.687337 8.301728
> colMax(tmp5)
[1] 465.01593 90.63928 82.20696 89.07495 89.84984 76.73728 87.82744
[8] 86.12372 83.00201 NA 79.16393 81.43992 89.09827 79.50576
[15] 91.39037 83.74811 88.94394 81.29354 89.64578 77.60473
> colMin(tmp5)
[1] 54.93184 58.66686 59.07373 55.17759 62.03446 59.49681 57.42254 59.90364
[9] 57.88467 NA 57.77154 62.10918 59.58540 58.97231 57.97628 65.18422
[17] 62.06139 62.59684 60.23069 53.93735
>
> Max(tmp5,na.rm=TRUE)
[1] 465.0159
> Min(tmp5,na.rm=TRUE)
[1] 53.93735
> mean(tmp5,na.rm=TRUE)
[1] 72.6814
> Sum(tmp5,na.rm=TRUE)
[1] 14463.6
> Var(tmp5,na.rm=TRUE)
[1] 850.4574
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.74693 70.60721 69.67674 69.76400 72.37864 71.00433 70.27500 68.99609
[9] 71.53797 70.64284
> rowSums(tmp5,na.rm=TRUE)
[1] 1834.939 1412.144 1393.535 1395.280 1447.573 1420.087 1405.500 1310.926
[9] 1430.759 1412.857
> rowVars(tmp5,na.rm=TRUE)
[1] 7805.33106 67.38415 72.20997 47.85148 52.05264 68.23065
[7] 94.44699 81.42833 65.34513 78.56503
> rowSd(tmp5,na.rm=TRUE)
[1] 88.347785 8.208785 8.497645 6.917477 7.214752 8.260185 9.718384
[8] 9.023765 8.083633 8.863692
> rowMax(tmp5,na.rm=TRUE)
[1] 465.01593 86.12372 89.09827 80.55850 89.84984 85.22680 91.39037
[8] 89.07495 87.82744 88.94394
> rowMin(tmp5,na.rm=TRUE)
[1] 57.42254 58.97231 57.77154 54.93184 58.84999 58.66686 55.17759 56.37612
[9] 61.35022 53.93735
>
> colMeans(tmp5,na.rm=TRUE)
[1] 109.38904 72.78300 71.46567 74.42178 73.10344 68.01596 68.67709
[8] 73.82796 71.73673 71.01780 68.62695 68.71344 73.49943 68.37758
[15] 70.12333 71.51517 72.14498 70.11445 70.04049 65.86737
> colSums(tmp5,na.rm=TRUE)
[1] 1093.8904 727.8300 714.6567 744.2178 731.0344 680.1596 686.7709
[8] 738.2796 717.3673 639.1602 686.2695 687.1344 734.9943 683.7758
[15] 701.2333 715.1517 721.4498 701.1445 700.4049 658.6737
> colVars(tmp5,na.rm=TRUE)
[1] 15678.29164 94.09892 55.87015 110.12705 80.76275 34.18202
[7] 96.72936 61.83663 69.99453 66.23058 62.41108 48.95746
[13] 86.79876 46.54192 150.21864 45.79741 69.25135 32.48132
[19] 75.46982 68.91868
> colSd(tmp5,na.rm=TRUE)
[1] 125.212985 9.700460 7.474634 10.494144 8.986810 5.846539
[7] 9.835109 7.863627 8.366273 8.138217 7.900068 6.996961
[13] 9.316585 6.822164 12.256371 6.767378 8.321739 5.699239
[19] 8.687337 8.301728
> colMax(tmp5,na.rm=TRUE)
[1] 465.01593 90.63928 82.20696 89.07495 89.84984 76.73728 87.82744
[8] 86.12372 83.00201 87.74877 79.16393 81.43992 89.09827 79.50576
[15] 91.39037 83.74811 88.94394 81.29354 89.64578 77.60473
> colMin(tmp5,na.rm=TRUE)
[1] 54.93184 58.66686 59.07373 55.17759 62.03446 59.49681 57.42254 59.90364
[9] 57.88467 61.80609 57.77154 62.10918 59.58540 58.97231 57.97628 65.18422
[17] 62.06139 62.59684 60.23069 53.93735
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.74693 70.60721 69.67674 69.76400 72.37864 71.00433 70.27500 NaN
[9] 71.53797 70.64284
> rowSums(tmp5,na.rm=TRUE)
[1] 1834.939 1412.144 1393.535 1395.280 1447.573 1420.087 1405.500 0.000
[9] 1430.759 1412.857
> rowVars(tmp5,na.rm=TRUE)
[1] 7805.33106 67.38415 72.20997 47.85148 52.05264 68.23065
[7] 94.44699 NA 65.34513 78.56503
> rowSd(tmp5,na.rm=TRUE)
[1] 88.347785 8.208785 8.497645 6.917477 7.214752 8.260185 9.718384
[8] NA 8.083633 8.863692
> rowMax(tmp5,na.rm=TRUE)
[1] 465.01593 86.12372 89.09827 80.55850 89.84984 85.22680 91.39037
[8] NA 87.82744 88.94394
> rowMin(tmp5,na.rm=TRUE)
[1] 57.42254 58.97231 57.77154 54.93184 58.84999 58.66686 55.17759 NA
[9] 61.35022 53.93735
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 114.45102 73.23045 72.38009 72.79365 74.33333 67.88849 69.52680
[8] 75.08415 71.43308 NaN 69.21853 69.44285 74.80487 67.14112
[15] 71.03135 70.15595 71.57214 69.54000 69.44048 66.92196
> colSums(tmp5,na.rm=TRUE)
[1] 1030.0592 659.0740 651.4209 655.1428 669.0000 610.9964 625.7412
[8] 675.7574 642.8977 0.0000 622.9668 624.9857 673.2439 604.2701
[15] 639.2821 631.4036 644.1493 625.8600 624.9643 602.2976
> colVars(tmp5,na.rm=TRUE)
[1] 17349.81171 103.60895 53.44693 94.07133 73.84109 38.27197
[7] 100.69783 51.81346 77.70653 NA 66.27541 49.09173
[13] 78.47658 35.16017 159.72029 30.73808 74.21621 32.82910
[19] 80.85342 65.02187
> colSd(tmp5,na.rm=TRUE)
[1] 131.718684 10.178848 7.310741 9.699038 8.593084 6.186435
[7] 10.034831 7.198157 8.815131 NA 8.140971 7.006549
[13] 8.858701 5.929602 12.638049 5.544193 8.614883 5.729669
[19] 8.991853 8.063614
> colMax(tmp5,na.rm=TRUE)
[1] 465.01593 90.63928 82.20696 85.22680 89.84984 76.73728 87.82744
[8] 86.12372 83.00201 -Inf 79.16393 81.43992 89.09827 77.21439
[15] 91.39037 80.55850 88.94394 81.29354 89.64578 77.60473
> colMin(tmp5,na.rm=TRUE)
[1] 54.93184 58.66686 59.07373 55.17759 62.29798 59.49681 57.42254 59.90364
[9] 57.88467 Inf 57.77154 62.10918 59.58540 58.97231 57.97628 65.18422
[17] 62.06139 62.59684 60.23069 53.93735
>
>
>
>
> 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] 214.62035 274.67829 252.11450 259.08816 277.51850 250.29012 70.33441
[8] 176.67983 176.10585 152.09552
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 214.62035 274.67829 252.11450 259.08816 277.51850 250.29012 70.33441
[8] 176.67983 176.10585 152.09552
>
>
>
> 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 2.131628e-14 -1.136868e-13 1.136868e-13 0.000000e+00
[6] 1.421085e-14 8.526513e-14 1.136868e-13 -4.263256e-14 -1.705303e-13
[11] -8.526513e-14 1.136868e-13 -5.684342e-14 -1.421085e-14 2.273737e-13
[16] 0.000000e+00 1.705303e-13 -2.842171e-13 -8.526513e-14 7.105427e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
8 6
6 16
4 14
9 4
3 9
8 5
8 17
7 3
2 3
3 12
8 5
8 14
10 4
10 10
10 6
3 1
10 10
4 1
3 13
10 4
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] 2.488608
> Min(tmp)
[1] -2.392832
> mean(tmp)
[1] -0.2279927
> Sum(tmp)
[1] -22.79927
> Var(tmp)
[1] 0.9178453
>
> rowMeans(tmp)
[1] -0.2279927
> rowSums(tmp)
[1] -22.79927
> rowVars(tmp)
[1] 0.9178453
> rowSd(tmp)
[1] 0.9580424
> rowMax(tmp)
[1] 2.488608
> rowMin(tmp)
[1] -2.392832
>
> colMeans(tmp)
[1] -0.62383853 1.02142147 -1.41283965 -0.29877534 -1.28791003 1.24256555
[7] 0.10750991 -0.94369588 0.91433246 -0.56120501 -0.20256064 -1.50736360
[13] 0.62708704 0.25563442 -1.15366450 -0.40588468 0.23630089 0.58789102
[19] 1.74737798 -1.39187561 0.73588578 -1.17243291 -1.66053919 0.54135884
[25] -1.40998388 0.41293444 -0.65871304 -0.33665834 0.55481231 -1.16015125
[31] 0.26492342 0.23353800 0.23194883 -0.42836382 -0.80321911 0.55502080
[37] 0.84934630 -0.35401591 0.65838068 1.75983138 -0.82063857 0.12984604
[43] 0.05658894 -0.49153393 -0.07136706 -0.16067754 0.48706627 -1.69755154
[49] 0.69524066 -0.64200646 -0.37055476 -0.97010050 2.48860762 -0.10583486
[55] -1.94144976 -1.25028525 -0.98211624 -0.85579679 -1.22624701 -1.48557817
[61] -0.92110449 -0.27926288 -0.18650164 -1.06973032 0.20500010 1.94949887
[67] -0.21794548 -0.40241666 -0.53483079 -0.55495524 0.85698521 1.34719837
[73] -0.44602803 -0.99804897 -0.76692843 -0.44085171 -2.39283227 -1.47381202
[79] -1.93236182 -1.31581919 0.65039590 0.04909101 0.51122820 0.21091881
[85] -0.53034903 -0.02457792 -0.24550093 -0.65403898 -0.17224123 1.18738172
[91] 0.22622025 -0.96987861 -0.48278220 -2.06838285 0.28240660 0.90026007
[97] 1.45094113 1.21447867 -1.42824149 0.11812879
> colSums(tmp)
[1] -0.62383853 1.02142147 -1.41283965 -0.29877534 -1.28791003 1.24256555
[7] 0.10750991 -0.94369588 0.91433246 -0.56120501 -0.20256064 -1.50736360
[13] 0.62708704 0.25563442 -1.15366450 -0.40588468 0.23630089 0.58789102
[19] 1.74737798 -1.39187561 0.73588578 -1.17243291 -1.66053919 0.54135884
[25] -1.40998388 0.41293444 -0.65871304 -0.33665834 0.55481231 -1.16015125
[31] 0.26492342 0.23353800 0.23194883 -0.42836382 -0.80321911 0.55502080
[37] 0.84934630 -0.35401591 0.65838068 1.75983138 -0.82063857 0.12984604
[43] 0.05658894 -0.49153393 -0.07136706 -0.16067754 0.48706627 -1.69755154
[49] 0.69524066 -0.64200646 -0.37055476 -0.97010050 2.48860762 -0.10583486
[55] -1.94144976 -1.25028525 -0.98211624 -0.85579679 -1.22624701 -1.48557817
[61] -0.92110449 -0.27926288 -0.18650164 -1.06973032 0.20500010 1.94949887
[67] -0.21794548 -0.40241666 -0.53483079 -0.55495524 0.85698521 1.34719837
[73] -0.44602803 -0.99804897 -0.76692843 -0.44085171 -2.39283227 -1.47381202
[79] -1.93236182 -1.31581919 0.65039590 0.04909101 0.51122820 0.21091881
[85] -0.53034903 -0.02457792 -0.24550093 -0.65403898 -0.17224123 1.18738172
[91] 0.22622025 -0.96987861 -0.48278220 -2.06838285 0.28240660 0.90026007
[97] 1.45094113 1.21447867 -1.42824149 0.11812879
> 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] -0.62383853 1.02142147 -1.41283965 -0.29877534 -1.28791003 1.24256555
[7] 0.10750991 -0.94369588 0.91433246 -0.56120501 -0.20256064 -1.50736360
[13] 0.62708704 0.25563442 -1.15366450 -0.40588468 0.23630089 0.58789102
[19] 1.74737798 -1.39187561 0.73588578 -1.17243291 -1.66053919 0.54135884
[25] -1.40998388 0.41293444 -0.65871304 -0.33665834 0.55481231 -1.16015125
[31] 0.26492342 0.23353800 0.23194883 -0.42836382 -0.80321911 0.55502080
[37] 0.84934630 -0.35401591 0.65838068 1.75983138 -0.82063857 0.12984604
[43] 0.05658894 -0.49153393 -0.07136706 -0.16067754 0.48706627 -1.69755154
[49] 0.69524066 -0.64200646 -0.37055476 -0.97010050 2.48860762 -0.10583486
[55] -1.94144976 -1.25028525 -0.98211624 -0.85579679 -1.22624701 -1.48557817
[61] -0.92110449 -0.27926288 -0.18650164 -1.06973032 0.20500010 1.94949887
[67] -0.21794548 -0.40241666 -0.53483079 -0.55495524 0.85698521 1.34719837
[73] -0.44602803 -0.99804897 -0.76692843 -0.44085171 -2.39283227 -1.47381202
[79] -1.93236182 -1.31581919 0.65039590 0.04909101 0.51122820 0.21091881
[85] -0.53034903 -0.02457792 -0.24550093 -0.65403898 -0.17224123 1.18738172
[91] 0.22622025 -0.96987861 -0.48278220 -2.06838285 0.28240660 0.90026007
[97] 1.45094113 1.21447867 -1.42824149 0.11812879
> colMin(tmp)
[1] -0.62383853 1.02142147 -1.41283965 -0.29877534 -1.28791003 1.24256555
[7] 0.10750991 -0.94369588 0.91433246 -0.56120501 -0.20256064 -1.50736360
[13] 0.62708704 0.25563442 -1.15366450 -0.40588468 0.23630089 0.58789102
[19] 1.74737798 -1.39187561 0.73588578 -1.17243291 -1.66053919 0.54135884
[25] -1.40998388 0.41293444 -0.65871304 -0.33665834 0.55481231 -1.16015125
[31] 0.26492342 0.23353800 0.23194883 -0.42836382 -0.80321911 0.55502080
[37] 0.84934630 -0.35401591 0.65838068 1.75983138 -0.82063857 0.12984604
[43] 0.05658894 -0.49153393 -0.07136706 -0.16067754 0.48706627 -1.69755154
[49] 0.69524066 -0.64200646 -0.37055476 -0.97010050 2.48860762 -0.10583486
[55] -1.94144976 -1.25028525 -0.98211624 -0.85579679 -1.22624701 -1.48557817
[61] -0.92110449 -0.27926288 -0.18650164 -1.06973032 0.20500010 1.94949887
[67] -0.21794548 -0.40241666 -0.53483079 -0.55495524 0.85698521 1.34719837
[73] -0.44602803 -0.99804897 -0.76692843 -0.44085171 -2.39283227 -1.47381202
[79] -1.93236182 -1.31581919 0.65039590 0.04909101 0.51122820 0.21091881
[85] -0.53034903 -0.02457792 -0.24550093 -0.65403898 -0.17224123 1.18738172
[91] 0.22622025 -0.96987861 -0.48278220 -2.06838285 0.28240660 0.90026007
[97] 1.45094113 1.21447867 -1.42824149 0.11812879
> colMedians(tmp)
[1] -0.62383853 1.02142147 -1.41283965 -0.29877534 -1.28791003 1.24256555
[7] 0.10750991 -0.94369588 0.91433246 -0.56120501 -0.20256064 -1.50736360
[13] 0.62708704 0.25563442 -1.15366450 -0.40588468 0.23630089 0.58789102
[19] 1.74737798 -1.39187561 0.73588578 -1.17243291 -1.66053919 0.54135884
[25] -1.40998388 0.41293444 -0.65871304 -0.33665834 0.55481231 -1.16015125
[31] 0.26492342 0.23353800 0.23194883 -0.42836382 -0.80321911 0.55502080
[37] 0.84934630 -0.35401591 0.65838068 1.75983138 -0.82063857 0.12984604
[43] 0.05658894 -0.49153393 -0.07136706 -0.16067754 0.48706627 -1.69755154
[49] 0.69524066 -0.64200646 -0.37055476 -0.97010050 2.48860762 -0.10583486
[55] -1.94144976 -1.25028525 -0.98211624 -0.85579679 -1.22624701 -1.48557817
[61] -0.92110449 -0.27926288 -0.18650164 -1.06973032 0.20500010 1.94949887
[67] -0.21794548 -0.40241666 -0.53483079 -0.55495524 0.85698521 1.34719837
[73] -0.44602803 -0.99804897 -0.76692843 -0.44085171 -2.39283227 -1.47381202
[79] -1.93236182 -1.31581919 0.65039590 0.04909101 0.51122820 0.21091881
[85] -0.53034903 -0.02457792 -0.24550093 -0.65403898 -0.17224123 1.18738172
[91] 0.22622025 -0.96987861 -0.48278220 -2.06838285 0.28240660 0.90026007
[97] 1.45094113 1.21447867 -1.42824149 0.11812879
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -0.6238385 1.021421 -1.41284 -0.2987753 -1.28791 1.242566 0.1075099
[2,] -0.6238385 1.021421 -1.41284 -0.2987753 -1.28791 1.242566 0.1075099
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.9436959 0.9143325 -0.561205 -0.2025606 -1.507364 0.627087 0.2556344
[2,] -0.9436959 0.9143325 -0.561205 -0.2025606 -1.507364 0.627087 0.2556344
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -1.153664 -0.4058847 0.2363009 0.587891 1.747378 -1.391876 0.7358858
[2,] -1.153664 -0.4058847 0.2363009 0.587891 1.747378 -1.391876 0.7358858
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -1.172433 -1.660539 0.5413588 -1.409984 0.4129344 -0.658713 -0.3366583
[2,] -1.172433 -1.660539 0.5413588 -1.409984 0.4129344 -0.658713 -0.3366583
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.5548123 -1.160151 0.2649234 0.233538 0.2319488 -0.4283638 -0.8032191
[2,] 0.5548123 -1.160151 0.2649234 0.233538 0.2319488 -0.4283638 -0.8032191
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.5550208 0.8493463 -0.3540159 0.6583807 1.759831 -0.8206386 0.129846
[2,] 0.5550208 0.8493463 -0.3540159 0.6583807 1.759831 -0.8206386 0.129846
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.05658894 -0.4915339 -0.07136706 -0.1606775 0.4870663 -1.697552 0.6952407
[2,] 0.05658894 -0.4915339 -0.07136706 -0.1606775 0.4870663 -1.697552 0.6952407
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -0.6420065 -0.3705548 -0.9701005 2.488608 -0.1058349 -1.94145 -1.250285
[2,] -0.6420065 -0.3705548 -0.9701005 2.488608 -0.1058349 -1.94145 -1.250285
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -0.9821162 -0.8557968 -1.226247 -1.485578 -0.9211045 -0.2792629 -0.1865016
[2,] -0.9821162 -0.8557968 -1.226247 -1.485578 -0.9211045 -0.2792629 -0.1865016
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -1.06973 0.2050001 1.949499 -0.2179455 -0.4024167 -0.5348308 -0.5549552
[2,] -1.06973 0.2050001 1.949499 -0.2179455 -0.4024167 -0.5348308 -0.5549552
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 0.8569852 1.347198 -0.446028 -0.998049 -0.7669284 -0.4408517 -2.392832
[2,] 0.8569852 1.347198 -0.446028 -0.998049 -0.7669284 -0.4408517 -2.392832
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -1.473812 -1.932362 -1.315819 0.6503959 0.04909101 0.5112282 0.2109188
[2,] -1.473812 -1.932362 -1.315819 0.6503959 0.04909101 0.5112282 0.2109188
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -0.530349 -0.02457792 -0.2455009 -0.654039 -0.1722412 1.187382 0.2262203
[2,] -0.530349 -0.02457792 -0.2455009 -0.654039 -0.1722412 1.187382 0.2262203
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.9698786 -0.4827822 -2.068383 0.2824066 0.9002601 1.450941 1.214479
[2,] -0.9698786 -0.4827822 -2.068383 0.2824066 0.9002601 1.450941 1.214479
[,99] [,100]
[1,] -1.428241 0.1181288
[2,] -1.428241 0.1181288
>
>
> Max(tmp2)
[1] 1.744275
> Min(tmp2)
[1] -2.139616
> mean(tmp2)
[1] -0.04747065
> Sum(tmp2)
[1] -4.747065
> Var(tmp2)
[1] 0.7505956
>
> rowMeans(tmp2)
[1] 0.416004932 -0.619158224 0.224693712 -0.124255879 0.960415286
[6] 0.097829522 0.364745521 -1.173949912 0.183231187 -0.473611186
[11] -0.990352433 0.012442863 1.609131760 0.162402568 -0.454048643
[16] 0.465459317 0.583892162 -0.756810968 1.434921193 0.836563673
[21] -0.430738692 0.446644003 0.191367454 0.438449262 -2.139616260
[26] 0.496198971 0.728414463 0.338909910 0.009578063 1.744274978
[31] 0.947345849 -0.059338253 -0.086187703 0.072487404 -0.587308701
[36] -1.326789159 -0.973588763 0.795566168 0.687206892 -0.443358928
[41] -0.180786227 -1.544661812 -1.383545820 0.193171986 -0.577091819
[46] -0.157073679 0.270893544 -0.708936043 -0.158850925 0.769025129
[51] 0.429001086 -0.769931749 -0.743921121 1.190754433 1.689852994
[56] -0.126154720 0.319272111 0.504063353 1.626702378 0.710473417
[61] 0.483304712 -1.310787138 -0.724733958 1.394071619 0.555966284
[66] -0.410736319 -1.194265977 0.165236637 0.605195494 0.118934858
[71] -1.648851842 -0.599492430 -0.756597981 1.431781531 0.266982997
[76] -0.725215799 0.754185294 -0.152522662 -0.735486715 0.288065392
[81] -0.279765455 0.049731806 1.667030659 -1.276009333 0.254570946
[86] -1.708963014 0.560353661 -0.566286406 -1.014037863 -0.251396613
[91] 0.112584646 -1.454213622 -0.613136142 0.267935288 -1.256241650
[96] -1.361217279 -0.214381989 -1.332321803 -0.643682721 1.546028334
> rowSums(tmp2)
[1] 0.416004932 -0.619158224 0.224693712 -0.124255879 0.960415286
[6] 0.097829522 0.364745521 -1.173949912 0.183231187 -0.473611186
[11] -0.990352433 0.012442863 1.609131760 0.162402568 -0.454048643
[16] 0.465459317 0.583892162 -0.756810968 1.434921193 0.836563673
[21] -0.430738692 0.446644003 0.191367454 0.438449262 -2.139616260
[26] 0.496198971 0.728414463 0.338909910 0.009578063 1.744274978
[31] 0.947345849 -0.059338253 -0.086187703 0.072487404 -0.587308701
[36] -1.326789159 -0.973588763 0.795566168 0.687206892 -0.443358928
[41] -0.180786227 -1.544661812 -1.383545820 0.193171986 -0.577091819
[46] -0.157073679 0.270893544 -0.708936043 -0.158850925 0.769025129
[51] 0.429001086 -0.769931749 -0.743921121 1.190754433 1.689852994
[56] -0.126154720 0.319272111 0.504063353 1.626702378 0.710473417
[61] 0.483304712 -1.310787138 -0.724733958 1.394071619 0.555966284
[66] -0.410736319 -1.194265977 0.165236637 0.605195494 0.118934858
[71] -1.648851842 -0.599492430 -0.756597981 1.431781531 0.266982997
[76] -0.725215799 0.754185294 -0.152522662 -0.735486715 0.288065392
[81] -0.279765455 0.049731806 1.667030659 -1.276009333 0.254570946
[86] -1.708963014 0.560353661 -0.566286406 -1.014037863 -0.251396613
[91] 0.112584646 -1.454213622 -0.613136142 0.267935288 -1.256241650
[96] -1.361217279 -0.214381989 -1.332321803 -0.643682721 1.546028334
> 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] 0.416004932 -0.619158224 0.224693712 -0.124255879 0.960415286
[6] 0.097829522 0.364745521 -1.173949912 0.183231187 -0.473611186
[11] -0.990352433 0.012442863 1.609131760 0.162402568 -0.454048643
[16] 0.465459317 0.583892162 -0.756810968 1.434921193 0.836563673
[21] -0.430738692 0.446644003 0.191367454 0.438449262 -2.139616260
[26] 0.496198971 0.728414463 0.338909910 0.009578063 1.744274978
[31] 0.947345849 -0.059338253 -0.086187703 0.072487404 -0.587308701
[36] -1.326789159 -0.973588763 0.795566168 0.687206892 -0.443358928
[41] -0.180786227 -1.544661812 -1.383545820 0.193171986 -0.577091819
[46] -0.157073679 0.270893544 -0.708936043 -0.158850925 0.769025129
[51] 0.429001086 -0.769931749 -0.743921121 1.190754433 1.689852994
[56] -0.126154720 0.319272111 0.504063353 1.626702378 0.710473417
[61] 0.483304712 -1.310787138 -0.724733958 1.394071619 0.555966284
[66] -0.410736319 -1.194265977 0.165236637 0.605195494 0.118934858
[71] -1.648851842 -0.599492430 -0.756597981 1.431781531 0.266982997
[76] -0.725215799 0.754185294 -0.152522662 -0.735486715 0.288065392
[81] -0.279765455 0.049731806 1.667030659 -1.276009333 0.254570946
[86] -1.708963014 0.560353661 -0.566286406 -1.014037863 -0.251396613
[91] 0.112584646 -1.454213622 -0.613136142 0.267935288 -1.256241650
[96] -1.361217279 -0.214381989 -1.332321803 -0.643682721 1.546028334
> rowMin(tmp2)
[1] 0.416004932 -0.619158224 0.224693712 -0.124255879 0.960415286
[6] 0.097829522 0.364745521 -1.173949912 0.183231187 -0.473611186
[11] -0.990352433 0.012442863 1.609131760 0.162402568 -0.454048643
[16] 0.465459317 0.583892162 -0.756810968 1.434921193 0.836563673
[21] -0.430738692 0.446644003 0.191367454 0.438449262 -2.139616260
[26] 0.496198971 0.728414463 0.338909910 0.009578063 1.744274978
[31] 0.947345849 -0.059338253 -0.086187703 0.072487404 -0.587308701
[36] -1.326789159 -0.973588763 0.795566168 0.687206892 -0.443358928
[41] -0.180786227 -1.544661812 -1.383545820 0.193171986 -0.577091819
[46] -0.157073679 0.270893544 -0.708936043 -0.158850925 0.769025129
[51] 0.429001086 -0.769931749 -0.743921121 1.190754433 1.689852994
[56] -0.126154720 0.319272111 0.504063353 1.626702378 0.710473417
[61] 0.483304712 -1.310787138 -0.724733958 1.394071619 0.555966284
[66] -0.410736319 -1.194265977 0.165236637 0.605195494 0.118934858
[71] -1.648851842 -0.599492430 -0.756597981 1.431781531 0.266982997
[76] -0.725215799 0.754185294 -0.152522662 -0.735486715 0.288065392
[81] -0.279765455 0.049731806 1.667030659 -1.276009333 0.254570946
[86] -1.708963014 0.560353661 -0.566286406 -1.014037863 -0.251396613
[91] 0.112584646 -1.454213622 -0.613136142 0.267935288 -1.256241650
[96] -1.361217279 -0.214381989 -1.332321803 -0.643682721 1.546028334
>
> colMeans(tmp2)
[1] -0.04747065
> colSums(tmp2)
[1] -4.747065
> colVars(tmp2)
[1] 0.7505956
> colSd(tmp2)
[1] 0.8663692
> colMax(tmp2)
[1] 1.744275
> colMin(tmp2)
[1] -2.139616
> colMedians(tmp2)
[1] 0.03108733
> colRanges(tmp2)
[,1]
[1,] -2.139616
[2,] 1.744275
>
> 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] 0.7663924 3.6135574 -3.8624263 -0.6787987 -0.3548908 -3.3614122
[7] 2.8224395 -0.4510922 0.9407430 2.1254972
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.7787391
[2,] -0.3347348
[3,] 0.1233143
[4,] 0.4810447
[5,] 0.7838111
>
> rowApply(tmp,sum)
[1] 2.7016011 1.7500468 5.1043628 -5.3582546 -4.9751821 3.5041732
[7] -1.2550383 1.0235414 -1.2158847 0.2806435
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 4 8 5 5 4 7 7 5 7 6
[2,] 10 2 8 8 8 9 4 8 3 9
[3,] 3 3 3 2 10 1 9 4 2 3
[4,] 5 10 1 1 3 10 5 2 5 1
[5,] 1 4 9 10 2 3 2 3 6 8
[6,] 2 9 4 6 5 2 1 6 4 4
[7,] 8 7 6 4 7 6 3 7 8 10
[8,] 7 5 7 3 1 5 10 10 1 5
[9,] 9 6 2 7 6 4 8 9 10 2
[10,] 6 1 10 9 9 8 6 1 9 7
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -2.1682075 -1.7898680 0.6649942 -1.4983304 -0.1273914 -0.1339844
[7] 1.2716699 -1.4006672 2.3075781 0.4917911 4.0988611 -0.2665613
[13] -0.3763888 -0.8660339 -3.4983523 -1.4417484 -2.8445891 -2.2605090
[19] -1.2187590 -0.3984600
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.0175594
[2,] -1.0173917
[3,] -0.8492966
[4,] -0.1665819
[5,] 0.8826222
>
> rowApply(tmp,sum)
[1] -1.431093 -9.143541 -5.977398 7.142186 -2.045110
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 3 6 7 8 17
[2,] 7 13 4 4 16
[3,] 16 15 15 11 9
[4,] 20 7 11 1 3
[5,] 6 4 10 12 19
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -1.0173917 -0.5017402 0.4848820 2.0066627 -0.6606607 0.3636299
[2,] -1.0175594 -0.1831561 0.1794360 -0.9836434 -1.2738581 0.7999030
[3,] -0.8492966 -1.2053013 0.2136107 -0.1391186 -0.1955148 -1.1261482
[4,] -0.1665819 -0.5370594 0.1886381 -1.2284600 0.4302180 -0.5954749
[5,] 0.8826222 0.6373890 -0.4015726 -1.1537711 1.5724242 0.4241058
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -0.1293048 1.23492018 1.14591545 0.1702375 0.1381934 0.7407917
[2,] 0.4462717 -0.04485518 0.68292459 -1.9619391 -1.3183545 -0.5824823
[3,] 0.3366522 -1.72370758 -0.47897929 0.1634325 -0.2385763 -1.6662636
[4,] 1.1827440 -0.37140866 0.99162693 1.2363268 3.9099442 0.9791777
[5,] -0.5646931 -0.49561598 -0.03390957 0.8837334 1.6076541 0.2622153
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.059365653 -0.92516486 -0.19995605 -0.05233582 -1.5105152 -0.43968359
[2,] -0.830870227 -0.23886665 -2.01005013 -1.24948638 0.1858561 -0.19967757
[3,] 0.483202760 0.04362732 0.05681777 1.34248212 0.9967771 -1.02244319
[4,] -0.079301176 1.40806369 -0.27883661 -0.18261162 -1.0586070 -0.06330421
[5,] -0.008785817 -1.15369342 -1.06632726 -1.29979670 -1.4581001 -0.53540044
[,19] [,20]
[1,] -1.5588164 -0.7801226
[2,] -0.9487197 1.4055860
[3,] 0.5360956 -1.5047461
[4,] 0.6068221 0.7702700
[5,] 0.1458594 -0.2894473
>
>
> 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 : 652 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 0.914831 -1.25513 -0.1275973 -1.193022 0.7337835 0.6460699 0.250805
col8 col9 col10 col11 col12 col13 col14
row1 0.6679118 -2.254408 0.3060149 1.318542 0.2361649 0.8654071 -0.2644399
col15 col16 col17 col18 col19 col20
row1 -0.181467 -0.581402 -0.3004331 1.103679 1.323738 0.2042724
> tmp[,"col10"]
col10
row1 0.30601486
row2 -0.99904851
row3 -1.34531392
row4 -0.42367311
row5 0.03569831
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 0.9148310 -1.2551303 -0.1275973 -1.19302195 0.7337835 0.64606985
row5 -0.2083816 0.7781558 -0.1270265 -0.03285054 1.0591361 0.03511549
col7 col8 col9 col10 col11 col12 col13
row1 0.2508050 0.6679118 -2.2544083 0.30601486 1.3185423 0.2361649 0.8654071
row5 0.1728338 -0.1943329 -0.2610358 0.03569831 0.5944159 0.6698256 0.8545839
col14 col15 col16 col17 col18 col19
row1 -0.26443988 -0.181467 -0.5814020 -0.3004331 1.1036789 1.3237381
row5 0.08640658 -0.730391 -0.1342089 -0.1040708 -0.8891935 -0.3029283
col20
row1 0.2042724
row5 0.4835962
> tmp[,c("col6","col20")]
col6 col20
row1 0.64606985 0.20427240
row2 -0.97136331 1.12000650
row3 -0.50953987 0.46244748
row4 0.81435969 -0.05452471
row5 0.03511549 0.48359624
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.64606985 0.2042724
row5 0.03511549 0.4835962
>
>
>
>
> 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 48.6284 49.76114 52.2423 50.12828 49.47971 105.9124 49.6961 50.19162
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.48541 49.17619 50.62451 49.57936 51.24725 50.63954 48.54481 51.72715
col17 col18 col19 col20
row1 50.55973 49.22555 48.77963 104.7365
> tmp[,"col10"]
col10
row1 49.17619
row2 28.69896
row3 31.10498
row4 28.67294
row5 50.18098
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 48.62840 49.76114 52.24230 50.12828 49.47971 105.9124 49.69610 50.19162
row5 49.60088 50.20452 49.05526 51.04487 49.28144 106.1419 49.79339 49.24048
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.48541 49.17619 50.62451 49.57936 51.24725 50.63954 48.54481 51.72715
row5 50.02341 50.18098 50.53652 51.55824 50.19750 49.34648 49.54091 50.88924
col17 col18 col19 col20
row1 50.55973 49.22555 48.77963 104.7365
row5 51.01493 50.46204 48.39129 104.4763
> tmp[,c("col6","col20")]
col6 col20
row1 105.91243 104.73646
row2 74.01068 75.80106
row3 72.51599 73.98089
row4 76.18677 72.81739
row5 106.14191 104.47625
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.9124 104.7365
row5 106.1419 104.4763
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.9124 104.7365
row5 106.1419 104.4763
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.1484487
[2,] 1.1480171
[3,] -0.5204172
[4,] -1.5535025
[5,] -0.7272735
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.49609492 1.10893211
[2,] 0.73517897 -0.74621114
[3,] 0.51396116 -0.96685889
[4,] 0.05133326 0.02103265
[5,] 0.35756074 -0.43099330
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.6479640 -0.086992455
[2,] 0.4418300 0.002628989
[3,] 0.5606543 -0.367587391
[4,] -2.1799957 0.754817673
[5,] 0.5327638 -0.364279770
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.647964
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.647964
[2,] 0.441830
>
>
>
> 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 0.2789024 0.5290548 -1.4949503 1.2920120 1.616695 0.5939806 -0.8502856
row1 1.0467405 0.2553498 0.3138498 -0.9183254 -1.096542 0.3755125 0.1082766
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row3 0.8892578 0.953505 0.9641703 -0.5391687 0.2586770 -0.2023462 -0.4417988
row1 -0.3836855 -0.241674 1.0237861 -0.2077215 0.2498816 1.6192114 0.2737242
[,15] [,16] [,17] [,18] [,19] [,20]
row3 -0.4608334 -1.234031 1.9616203 -0.06587895 0.02809888 -0.6983796
row1 0.1917132 1.758221 0.6863547 0.48811852 -1.11297266 0.4182713
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -1.379364 -0.3825567 -1.652808 1.533814 0.1158927 -1.430669 0.3409014
[,8] [,9] [,10]
row2 1.739954 -0.8514876 1.13163
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.01928458 -0.2145665 -0.374533 -2.926267 -0.4620017 0.9337004 0.3021034
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.8695527 1.277334 0.04646882 -0.7183839 0.5674291 0.2597235 -0.8087091
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.5600733 -0.6539788 -2.117657 0.6144904 0.7304037 -0.7758941
>
>
> 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: 0x5a7475bbc0a0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2382082ec0a756"
[2] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM238208e6eb0d0"
[3] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM23820815be71dc"
[4] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM238208270836b3"
[5] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2382082a517faa"
[6] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2382082578fc7d"
[7] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM23820844d0c2ad"
[8] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM23820841c4ed34"
[9] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM238208a5d728d"
[10] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2382082d22842e"
[11] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2382081a9d8080"
[12] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM23820860918523"
[13] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2382081c85b849"
[14] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM238208624748bb"
[15] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM2382082dcb4586"
>
>
> ### 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: 0x5a7475d78090>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x5a7475d78090>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x5a7475d78090>
> rowMedians(tmp)
[1] 0.293586594 0.140892474 0.054797711 0.028711393 -0.085851229
[6] -0.091905803 0.096346794 -0.485627609 0.876562171 0.391186619
[11] 0.365563005 0.321379909 -0.225416351 0.405026423 0.379630155
[16] -0.087699693 -0.318015546 0.270685310 -0.186592350 -0.004165359
[21] 0.190355262 -0.418162951 0.034134300 -0.885979994 0.125074697
[26] 0.148488398 0.089932645 0.313177108 0.304119549 0.253408789
[31] -0.354344184 0.054783873 -0.166748446 -0.242891130 0.654053623
[36] -0.272435329 0.290512748 -0.418353135 0.250180617 -0.118666475
[41] 0.140751857 0.022173240 0.363039692 -0.052785235 0.368070619
[46] 0.225318968 0.062108556 -0.019140237 -0.065428887 0.164382515
[51] 0.228380577 0.279070895 -0.021113074 0.247098105 -0.388973234
[56] -0.512727693 0.108901428 -0.228263474 0.037452706 -0.303077166
[61] 0.036540185 0.161415027 -0.249738797 0.328925832 0.221331681
[66] -0.357069661 0.125916169 -0.102579216 0.091926106 0.261651944
[71] 0.764487997 0.178045254 0.193465741 -0.570473758 0.452159186
[76] -0.178225953 -0.177397100 0.129614505 0.039748016 -0.402350402
[81] -0.331713638 0.252518607 -0.268952164 0.104735867 -0.102511498
[86] -0.144966518 0.393592817 -0.297575431 -0.680558023 -0.451856202
[91] -0.375303933 -0.014664824 0.123981142 -0.441459794 -0.352602499
[96] 0.161075326 -0.226808858 0.054987294 0.755840353 0.433648559
[101] 0.488986974 0.519336890 -0.221321663 0.056822278 0.693783984
[106] 0.055925349 0.206046371 0.636193835 -0.695676262 -0.174071579
[111] 0.022632131 -0.020377904 -0.397841997 -0.276023884 -0.203523018
[116] -0.253065508 -0.067134783 0.433212980 -0.187842717 0.622980699
[121] 0.782399888 -0.212426387 -0.077751073 -0.393350161 0.384469121
[126] -0.098268843 0.295734724 0.044706326 0.522225337 0.158166781
[131] -0.155010729 0.489143434 0.084658360 -0.432353854 0.193897456
[136] 0.305872724 -0.127881726 -0.216661387 -0.027143807 -0.269714379
[141] -0.028313569 0.303061365 0.291217435 0.279364956 0.371440173
[146] -0.352600819 0.234721415 0.067063127 -0.375871350 -0.354927121
[151] 0.027425068 -0.375422335 0.228949338 -0.267224546 0.026593449
[156] -0.282082472 -0.132884617 0.250385712 -0.477374218 -0.059741033
[161] 0.061841168 0.314273498 0.085198131 0.311326133 -0.097722553
[166] -0.200973790 -0.078936367 0.073774047 -0.286162736 -0.034500346
[171] 0.082088102 0.108560900 -0.579086159 -0.100047174 0.066871728
[176] -0.384873536 0.622371782 0.193150609 0.424812925 -0.353591949
[181] -0.455871302 0.059610629 0.445192212 -0.488040965 -0.120792904
[186] 0.519768838 0.269290089 0.286540742 0.325557951 -0.154216435
[191] 0.184909051 -0.507671616 0.507336909 -0.727408209 0.345921419
[196] -0.480375229 0.056890518 0.384483087 0.018576224 -0.254903289
[201] -0.374142253 0.488285569 -0.070858074 0.355140173 -0.185085532
[206] 0.538961295 0.175210168 -0.023532017 -0.439781324 0.672814854
[211] -0.251137599 0.219384571 0.169312131 -0.064981554 0.027027276
[216] 0.349347346 0.250210387 0.018860022 0.685911636 0.368032573
[221] 0.230257682 -0.011043307 -0.051940286 0.191376571 0.130445654
[226] -0.041592866 0.083881464 -0.164447626 0.292802016 0.160611679
>
> proc.time()
user system elapsed
1.242 0.664 1.896
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: 0x5b9cec9ca370>
> .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: 0x5b9cec9ca370>
> .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: 0x5b9cec9ca370>
> .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: 0x5b9cec9ca370>
> 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: 0x5b9cec9b21c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b9cec9b21c0>
> .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: 0x5b9cec9b21c0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b9cec9b21c0>
> .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: 0x5b9cec9b21c0>
> 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: 0x5b9cecc95120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b9cecc95120>
> .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: 0x5b9cecc95120>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5b9cecc95120>
> .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: 0x5b9cecc95120>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x5b9cecc95120>
> .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: 0x5b9cecc95120>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x5b9cecc95120>
> .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: 0x5b9cecc95120>
> 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: 0x5b9ceb9e5390>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x5b9ceb9e5390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b9ceb9e5390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b9ceb9e5390>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile2383023e6ec08" "BufferedMatrixFile238302637a9da1"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile2383023e6ec08" "BufferedMatrixFile238302637a9da1"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b9ceb8dc3d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b9ceb8dc3d0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5b9ceb8dc3d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5b9ceb8dc3d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x5b9ceb8dc3d0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x5b9ceb8dc3d0>
> .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: 0x5b9ced411fa0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5b9ced411fa0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5b9ced411fa0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x5b9ced411fa0>
> 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: 0x5b9cebbe9ff0>
> .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: 0x5b9cebbe9ff0>
> rm(P)
>
> proc.time()
user system elapsed
0.267 0.035 0.291
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
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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
0.278 0.036 0.303