Ben Bolstad
| Snapshot Date: 2026-03-31 13:45 -0400 (Tue, 31 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_22 |
| git_last_commit: d2ce144 |
| git_last_commit_date: 2025-10-29 09:58:55 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-04-01 11:57 -0400 (Wed, 01 Apr 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" | 4896 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 257/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.74.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BufferedMatrix in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.74.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BufferedMatrix_1.74.0.tar.gz |
| StartedAt: 2026-03-31 21:38:25 -0400 (Tue, 31 Mar 2026) |
| EndedAt: 2026-03-31 21:38:49 -0400 (Tue, 31 Mar 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 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.74.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BufferedMatrix’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup?
209 | $x^{power}$ elementwise of the matrix
| ^
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘Rcodetesting.R’
Running ‘c_code_level_tests.R’
Running ‘objectTesting.R’
Running ‘rawCalltesting.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
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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 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function ‘dbm_ReadOnlyMode’:
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: ‘sort_double’ defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init_package.c -o init_package.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘rowSums’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colSums’ in package ‘BufferedMatrix’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘BufferedMatrix’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘BufferedMatrix’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix", "BufferedMatrix", .libPaths());.C("dbm_c_tester",integer(1))
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
Adding Additional Column
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000
Reassigning values
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 3
Buffer Cols: 3
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Activating Row Buffer
In row mode: 1
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Squaring Last Column
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
5.000000 10.000000 15.000000 20.000000 25.000000 900.000000
Square rooting Last Row, then turing off Row Buffer
In row mode: 0
Checking on value that should be not be in column buffer2.236068
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
2.236068 3.162278 3.872983 4.472136 5.000000 30.000000
Single Indexing. Assign each value its square
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Resizing Buffers Smaller
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Activating Row Mode.
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
Activating ReadOnly Mode.
The results of assignment is: 0
Printing matrix reversed.
900.000000 625.000000 400.000000 225.000000 100.000000 25.000000
841.000000 576.000000 361.000000 196.000000 81.000000 16.000000
784.000000 529.000000 324.000000 169.000000 64.000000 9.000000
729.000000 484.000000 289.000000 144.000000 49.000000 -30.000000
676.000000 441.000000 256.000000 121.000000 -20.000000 -10.000000
[[1]]
[1] 0
>
> proc.time()
user system elapsed
0.239 0.051 0.281
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 478284 25.6 1046725 56 639600 34.2
Vcells 884773 6.8 8388608 64 2081613 15.9
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Tue Mar 31 21:38:40 2026"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Tue Mar 31 21:38:40 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: 0x5689b74761c0>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Tue Mar 31 21:38:40 2026"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Tue Mar 31 21:38:40 2026"
>
> ColMode(tmp2)
<pointer: 0x5689b74761c0>
>
>
>
> ### 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,] 99.34496731 -0.14752824 0.68489120 1.9012288
[2,] 1.94018154 -0.53526936 0.02423765 -0.6053828
[3,] 0.01354895 -0.02401067 0.61651304 0.8528023
[4,] -0.22679756 2.42907983 -0.20389546 1.5696021
> 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 : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 99.34496731 0.14752824 0.68489120 1.9012288
[2,] 1.94018154 0.53526936 0.02423765 0.6053828
[3,] 0.01354895 0.02401067 0.61651304 0.8528023
[4,] 0.22679756 2.42907983 0.20389546 1.5696021
> 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 : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 9.9671946 0.3840940 0.8275815 1.3788505
[2,] 1.3929040 0.7316210 0.1556844 0.7780635
[3,] 0.1163999 0.1549538 0.7851834 0.9234729
[4,] 0.4762327 1.5585506 0.4515479 1.2528376
>
> 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 : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 224.01691 28.98847 33.96071 40.68973
[2,] 40.86922 32.85148 26.58108 33.38602
[3,] 26.17755 26.57355 33.46835 35.08753
[4,] 29.98912 43.01459 29.71937 39.09798
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x5689b81453b0>
> exp(tmp5)
<pointer: 0x5689b81453b0>
> log(tmp5,2)
<pointer: 0x5689b81453b0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 466.2619
> Min(tmp5)
[1] 54.48514
> mean(tmp5)
[1] 73.05201
> Sum(tmp5)
[1] 14610.4
> Var(tmp5)
[1] 853.9801
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 91.87925 70.00689 70.87201 72.56216 70.43736 72.71053 70.81253 73.59848
[9] 69.28761 68.35329
> rowSums(tmp5)
[1] 1837.585 1400.138 1417.440 1451.243 1408.747 1454.211 1416.251 1471.970
[9] 1385.752 1367.066
> rowVars(tmp5)
[1] 7830.20502 67.48192 62.65580 91.26124 68.91452 68.54905
[7] 66.94422 66.42783 87.23432 95.43813
> rowSd(tmp5)
[1] 88.488446 8.214738 7.915542 9.553075 8.301477 8.279435 8.181945
[8] 8.150327 9.339931 9.769244
> rowMax(tmp5)
[1] 466.26185 86.62707 82.40320 89.52922 84.53095 89.41440 91.29040
[8] 87.96513 90.22582 89.56879
> rowMin(tmp5)
[1] 56.51895 55.32504 54.48514 59.90795 56.28767 59.39479 54.94527 61.04647
[9] 54.76686 55.63741
>
> colMeans(tmp5)
[1] 111.42003 66.90965 69.51562 71.88728 72.03375 71.47223 70.46471
[8] 69.96799 70.66907 70.54208 70.99547 71.12731 75.01210 73.45216
[15] 73.12837 72.26753 70.61551 68.47474 70.19873 70.88592
> colSums(tmp5)
[1] 1114.2003 669.0965 695.1562 718.8728 720.3375 714.7223 704.6471
[8] 699.6799 706.6907 705.4208 709.9547 711.2731 750.1210 734.5216
[15] 731.2837 722.6753 706.1551 684.7474 701.9873 708.8592
> colVars(tmp5)
[1] 15660.57166 122.10193 79.34310 86.33451 69.15897 62.31223
[7] 72.90412 55.34485 38.44647 69.43494 108.79671 92.20982
[13] 95.26894 120.87750 41.44057 69.17002 54.65528 57.63736
[19] 47.25283 92.86530
> colSd(tmp5)
[1] 125.142206 11.049974 8.907474 9.291637 8.316187 7.893810
[7] 8.538391 7.439412 6.200522 8.332763 10.430566 9.602594
[13] 9.760581 10.994430 6.437435 8.316851 7.392921 7.591927
[19] 6.874069 9.636664
> colMax(tmp5)
[1] 466.26185 89.52922 89.56879 84.69035 86.62707 88.28446 82.14523
[8] 84.53095 85.21579 83.69807 86.70067 89.41440 90.22582 91.29040
[15] 82.32825 86.46013 82.40320 80.29263 80.18056 83.59446
> colMin(tmp5)
[1] 54.48514 55.30936 55.32504 59.38680 59.14540 59.37968 58.93196 60.29749
[9] 64.60543 55.89945 54.94527 58.22212 55.63741 60.09208 63.13991 63.07931
[17] 60.81798 56.51895 59.90795 54.76686
>
>
> ### 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] 91.87925 70.00689 70.87201 72.56216 70.43736 72.71053 NA 73.59848
[9] 69.28761 68.35329
> rowSums(tmp5)
[1] 1837.585 1400.138 1417.440 1451.243 1408.747 1454.211 NA 1471.970
[9] 1385.752 1367.066
> rowVars(tmp5)
[1] 7830.20502 67.48192 62.65580 91.26124 68.91452 68.54905
[7] 70.65046 66.42783 87.23432 95.43813
> rowSd(tmp5)
[1] 88.488446 8.214738 7.915542 9.553075 8.301477 8.279435 8.405383
[8] 8.150327 9.339931 9.769244
> rowMax(tmp5)
[1] 466.26185 86.62707 82.40320 89.52922 84.53095 89.41440 NA
[8] 87.96513 90.22582 89.56879
> rowMin(tmp5)
[1] 56.51895 55.32504 54.48514 59.90795 56.28767 59.39479 NA 61.04647
[9] 54.76686 55.63741
>
> colMeans(tmp5)
[1] 111.42003 66.90965 69.51562 71.88728 72.03375 71.47223 70.46471
[8] 69.96799 70.66907 NA 70.99547 71.12731 75.01210 73.45216
[15] 73.12837 72.26753 70.61551 68.47474 70.19873 70.88592
> colSums(tmp5)
[1] 1114.2003 669.0965 695.1562 718.8728 720.3375 714.7223 704.6471
[8] 699.6799 706.6907 NA 709.9547 711.2731 750.1210 734.5216
[15] 731.2837 722.6753 706.1551 684.7474 701.9873 708.8592
> colVars(tmp5)
[1] 15660.57166 122.10193 79.34310 86.33451 69.15897 62.31223
[7] 72.90412 55.34485 38.44647 NA 108.79671 92.20982
[13] 95.26894 120.87750 41.44057 69.17002 54.65528 57.63736
[19] 47.25283 92.86530
> colSd(tmp5)
[1] 125.142206 11.049974 8.907474 9.291637 8.316187 7.893810
[7] 8.538391 7.439412 6.200522 NA 10.430566 9.602594
[13] 9.760581 10.994430 6.437435 8.316851 7.392921 7.591927
[19] 6.874069 9.636664
> colMax(tmp5)
[1] 466.26185 89.52922 89.56879 84.69035 86.62707 88.28446 82.14523
[8] 84.53095 85.21579 NA 86.70067 89.41440 90.22582 91.29040
[15] 82.32825 86.46013 82.40320 80.29263 80.18056 83.59446
> colMin(tmp5)
[1] 54.48514 55.30936 55.32504 59.38680 59.14540 59.37968 58.93196 60.29749
[9] 64.60543 NA 54.94527 58.22212 55.63741 60.09208 63.13991 63.07931
[17] 60.81798 56.51895 59.90795 54.76686
>
> Max(tmp5,na.rm=TRUE)
[1] 466.2619
> Min(tmp5,na.rm=TRUE)
[1] 54.48514
> mean(tmp5,na.rm=TRUE)
[1] 73.06562
> Sum(tmp5,na.rm=TRUE)
[1] 14540.06
> Var(tmp5,na.rm=TRUE)
[1] 858.2559
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.87925 70.00689 70.87201 72.56216 70.43736 72.71053 70.83723 73.59848
[9] 69.28761 68.35329
> rowSums(tmp5,na.rm=TRUE)
[1] 1837.585 1400.138 1417.440 1451.243 1408.747 1454.211 1345.907 1471.970
[9] 1385.752 1367.066
> rowVars(tmp5,na.rm=TRUE)
[1] 7830.20502 67.48192 62.65580 91.26124 68.91452 68.54905
[7] 70.65046 66.42783 87.23432 95.43813
> rowSd(tmp5,na.rm=TRUE)
[1] 88.488446 8.214738 7.915542 9.553075 8.301477 8.279435 8.405383
[8] 8.150327 9.339931 9.769244
> rowMax(tmp5,na.rm=TRUE)
[1] 466.26185 86.62707 82.40320 89.52922 84.53095 89.41440 91.29040
[8] 87.96513 90.22582 89.56879
> rowMin(tmp5,na.rm=TRUE)
[1] 56.51895 55.32504 54.48514 59.90795 56.28767 59.39479 54.94527 61.04647
[9] 54.76686 55.63741
>
> colMeans(tmp5,na.rm=TRUE)
[1] 111.42003 66.90965 69.51562 71.88728 72.03375 71.47223 70.46471
[8] 69.96799 70.66907 70.56418 70.99547 71.12731 75.01210 73.45216
[15] 73.12837 72.26753 70.61551 68.47474 70.19873 70.88592
> colSums(tmp5,na.rm=TRUE)
[1] 1114.2003 669.0965 695.1562 718.8728 720.3375 714.7223 704.6471
[8] 699.6799 706.6907 635.0777 709.9547 711.2731 750.1210 734.5216
[15] 731.2837 722.6753 706.1551 684.7474 701.9873 708.8592
> colVars(tmp5,na.rm=TRUE)
[1] 15660.57166 122.10193 79.34310 86.33451 69.15897 62.31223
[7] 72.90412 55.34485 38.44647 78.10881 108.79671 92.20982
[13] 95.26894 120.87750 41.44057 69.17002 54.65528 57.63736
[19] 47.25283 92.86530
> colSd(tmp5,na.rm=TRUE)
[1] 125.142206 11.049974 8.907474 9.291637 8.316187 7.893810
[7] 8.538391 7.439412 6.200522 8.837919 10.430566 9.602594
[13] 9.760581 10.994430 6.437435 8.316851 7.392921 7.591927
[19] 6.874069 9.636664
> colMax(tmp5,na.rm=TRUE)
[1] 466.26185 89.52922 89.56879 84.69035 86.62707 88.28446 82.14523
[8] 84.53095 85.21579 83.69807 86.70067 89.41440 90.22582 91.29040
[15] 82.32825 86.46013 82.40320 80.29263 80.18056 83.59446
> colMin(tmp5,na.rm=TRUE)
[1] 54.48514 55.30936 55.32504 59.38680 59.14540 59.37968 58.93196 60.29749
[9] 64.60543 55.89945 54.94527 58.22212 55.63741 60.09208 63.13991 63.07931
[17] 60.81798 56.51895 59.90795 54.76686
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 91.87925 70.00689 70.87201 72.56216 70.43736 72.71053 NaN 73.59848
[9] 69.28761 68.35329
> rowSums(tmp5,na.rm=TRUE)
[1] 1837.585 1400.138 1417.440 1451.243 1408.747 1454.211 0.000 1471.970
[9] 1385.752 1367.066
> rowVars(tmp5,na.rm=TRUE)
[1] 7830.20502 67.48192 62.65580 91.26124 68.91452 68.54905
[7] NA 66.42783 87.23432 95.43813
> rowSd(tmp5,na.rm=TRUE)
[1] 88.488446 8.214738 7.915542 9.553075 8.301477 8.279435 NA
[8] 8.150327 9.339931 9.769244
> rowMax(tmp5,na.rm=TRUE)
[1] 466.26185 86.62707 82.40320 89.52922 84.53095 89.41440 NA
[8] 87.96513 90.22582 89.56879
> rowMin(tmp5,na.rm=TRUE)
[1] 56.51895 55.32504 54.48514 59.90795 56.28767 59.39479 NA 61.04647
[9] 54.76686 55.63741
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 117.28571 67.57965 69.45371 70.68109 72.26140 72.06308 70.64336
[8] 69.15561 69.97113 NaN 72.77882 71.14943 75.00949 71.47014
[15] 73.22514 72.91666 70.56076 67.88800 69.72902 71.63049
> colSums(tmp5,na.rm=TRUE)
[1] 1055.5714 608.2169 625.0833 636.1298 650.3526 648.5678 635.7903
[8] 622.4005 629.7402 0.0000 655.0094 640.3449 675.0854 643.2312
[15] 659.0263 656.2499 635.0468 610.9920 627.5612 644.6744
> colVars(tmp5,na.rm=TRUE)
[1] 17231.07287 132.31444 89.21786 80.75857 77.22085 66.17372
[7] 81.65806 54.83839 37.77222 NA 86.61728 103.73054
[13] 107.17748 91.79236 46.51528 73.07592 61.45346 60.96915
[19] 50.67734 98.23661
> colSd(tmp5,na.rm=TRUE)
[1] 131.267181 11.502801 9.445521 8.986577 8.787540 8.134723
[7] 9.036485 7.405294 6.145911 NA 9.306841 10.184819
[13] 10.352656 9.580833 6.820211 8.548445 7.839226 7.808274
[19] 7.118802 9.911438
> colMax(tmp5,na.rm=TRUE)
[1] 466.26185 89.52922 89.56879 84.69035 86.62707 88.28446 82.14523
[8] 84.53095 85.21579 -Inf 86.70067 89.41440 90.22582 87.96513
[15] 82.32825 86.46013 82.40320 80.29263 80.18056 83.59446
> colMin(tmp5,na.rm=TRUE)
[1] 54.48514 55.30936 55.32504 59.38680 59.14540 59.37968 58.93196 60.29749
[9] 64.60543 Inf 60.43381 58.22212 55.63741 60.09208 63.13991 63.07931
[17] 60.81798 56.51895 59.90795 54.76686
>
>
>
>
> 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] 172.2967 304.7604 149.0903 267.2457 233.5386 216.7207 154.2336 296.1324
[9] 127.8667 191.3211
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 172.2967 304.7604 149.0903 267.2457 233.5386 216.7207 154.2336 296.1324
[9] 127.8667 191.3211
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] 0.000000e+00 -2.842171e-14 -1.136868e-13 2.842171e-14 1.989520e-13
[6] -8.526513e-14 5.684342e-14 4.263256e-14 0.000000e+00 5.684342e-14
[11] -8.526513e-14 -5.684342e-14 2.842171e-14 1.136868e-13 8.526513e-14
[16] -5.684342e-14 1.421085e-14 5.684342e-14 5.684342e-14 8.526513e-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)
+ }
1 4
9 4
5 4
9 14
9 17
6 4
2 19
7 5
5 14
2 2
8 8
3 14
6 9
6 1
4 11
3 4
2 15
7 11
9 15
5 20
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 3.054453
> Min(tmp)
[1] -2.399969
> mean(tmp)
[1] 0.2742391
> Sum(tmp)
[1] 27.42391
> Var(tmp)
[1] 0.9716044
>
> rowMeans(tmp)
[1] 0.2742391
> rowSums(tmp)
[1] 27.42391
> rowVars(tmp)
[1] 0.9716044
> rowSd(tmp)
[1] 0.9856999
> rowMax(tmp)
[1] 3.054453
> rowMin(tmp)
[1] -2.399969
>
> colMeans(tmp)
[1] 0.674770764 -0.088170254 -1.260533189 0.024321427 0.374758131
[6] 1.404130258 1.023349575 -0.313441508 -0.762725967 -0.575472523
[11] 0.171010213 -0.517091407 0.176753724 0.864248867 3.054453190
[16] -0.894373022 1.003653883 1.200439522 0.801696154 1.518937735
[21] 0.419405767 -0.381707032 -1.443081865 -2.045137222 0.774436533
[26] -0.578004255 0.441175359 -1.176329073 -0.765489711 0.461434631
[31] -0.460697707 -2.399968915 2.321675288 0.885702083 -0.678171910
[36] -0.642182580 -0.783834460 -0.315627818 0.885875036 1.201463844
[41] 1.410654825 -0.389889774 -0.045977780 0.941134635 -0.665040644
[46] 0.970632374 0.578498013 0.254240467 1.082884297 -0.289104967
[51] -0.138969640 0.614071493 0.517732077 -0.471027085 0.304705203
[56] -0.689777824 0.337540772 0.537433873 1.149376135 -0.724757284
[61] 0.345551042 1.875188840 0.574337211 2.098875074 2.172795983
[66] -0.427499632 1.098867011 -0.500103225 -0.510400634 0.382004438
[71] 0.713564014 1.088631836 0.381256070 1.851770704 2.058940384
[76] 0.597017327 1.914805149 0.100880001 0.251013854 -1.001427426
[81] 0.967406760 -1.390758197 0.892304097 0.309140023 0.537778505
[86] 0.246276054 -0.773117269 0.734675331 0.988466613 -1.427911209
[91] -0.178238451 0.671793717 -0.361478146 0.317379756 -0.908538414
[96] -0.005703448 0.873436381 -0.895899837 1.403302419 1.471520161
> colSums(tmp)
[1] 0.674770764 -0.088170254 -1.260533189 0.024321427 0.374758131
[6] 1.404130258 1.023349575 -0.313441508 -0.762725967 -0.575472523
[11] 0.171010213 -0.517091407 0.176753724 0.864248867 3.054453190
[16] -0.894373022 1.003653883 1.200439522 0.801696154 1.518937735
[21] 0.419405767 -0.381707032 -1.443081865 -2.045137222 0.774436533
[26] -0.578004255 0.441175359 -1.176329073 -0.765489711 0.461434631
[31] -0.460697707 -2.399968915 2.321675288 0.885702083 -0.678171910
[36] -0.642182580 -0.783834460 -0.315627818 0.885875036 1.201463844
[41] 1.410654825 -0.389889774 -0.045977780 0.941134635 -0.665040644
[46] 0.970632374 0.578498013 0.254240467 1.082884297 -0.289104967
[51] -0.138969640 0.614071493 0.517732077 -0.471027085 0.304705203
[56] -0.689777824 0.337540772 0.537433873 1.149376135 -0.724757284
[61] 0.345551042 1.875188840 0.574337211 2.098875074 2.172795983
[66] -0.427499632 1.098867011 -0.500103225 -0.510400634 0.382004438
[71] 0.713564014 1.088631836 0.381256070 1.851770704 2.058940384
[76] 0.597017327 1.914805149 0.100880001 0.251013854 -1.001427426
[81] 0.967406760 -1.390758197 0.892304097 0.309140023 0.537778505
[86] 0.246276054 -0.773117269 0.734675331 0.988466613 -1.427911209
[91] -0.178238451 0.671793717 -0.361478146 0.317379756 -0.908538414
[96] -0.005703448 0.873436381 -0.895899837 1.403302419 1.471520161
> 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] 0.674770764 -0.088170254 -1.260533189 0.024321427 0.374758131
[6] 1.404130258 1.023349575 -0.313441508 -0.762725967 -0.575472523
[11] 0.171010213 -0.517091407 0.176753724 0.864248867 3.054453190
[16] -0.894373022 1.003653883 1.200439522 0.801696154 1.518937735
[21] 0.419405767 -0.381707032 -1.443081865 -2.045137222 0.774436533
[26] -0.578004255 0.441175359 -1.176329073 -0.765489711 0.461434631
[31] -0.460697707 -2.399968915 2.321675288 0.885702083 -0.678171910
[36] -0.642182580 -0.783834460 -0.315627818 0.885875036 1.201463844
[41] 1.410654825 -0.389889774 -0.045977780 0.941134635 -0.665040644
[46] 0.970632374 0.578498013 0.254240467 1.082884297 -0.289104967
[51] -0.138969640 0.614071493 0.517732077 -0.471027085 0.304705203
[56] -0.689777824 0.337540772 0.537433873 1.149376135 -0.724757284
[61] 0.345551042 1.875188840 0.574337211 2.098875074 2.172795983
[66] -0.427499632 1.098867011 -0.500103225 -0.510400634 0.382004438
[71] 0.713564014 1.088631836 0.381256070 1.851770704 2.058940384
[76] 0.597017327 1.914805149 0.100880001 0.251013854 -1.001427426
[81] 0.967406760 -1.390758197 0.892304097 0.309140023 0.537778505
[86] 0.246276054 -0.773117269 0.734675331 0.988466613 -1.427911209
[91] -0.178238451 0.671793717 -0.361478146 0.317379756 -0.908538414
[96] -0.005703448 0.873436381 -0.895899837 1.403302419 1.471520161
> colMin(tmp)
[1] 0.674770764 -0.088170254 -1.260533189 0.024321427 0.374758131
[6] 1.404130258 1.023349575 -0.313441508 -0.762725967 -0.575472523
[11] 0.171010213 -0.517091407 0.176753724 0.864248867 3.054453190
[16] -0.894373022 1.003653883 1.200439522 0.801696154 1.518937735
[21] 0.419405767 -0.381707032 -1.443081865 -2.045137222 0.774436533
[26] -0.578004255 0.441175359 -1.176329073 -0.765489711 0.461434631
[31] -0.460697707 -2.399968915 2.321675288 0.885702083 -0.678171910
[36] -0.642182580 -0.783834460 -0.315627818 0.885875036 1.201463844
[41] 1.410654825 -0.389889774 -0.045977780 0.941134635 -0.665040644
[46] 0.970632374 0.578498013 0.254240467 1.082884297 -0.289104967
[51] -0.138969640 0.614071493 0.517732077 -0.471027085 0.304705203
[56] -0.689777824 0.337540772 0.537433873 1.149376135 -0.724757284
[61] 0.345551042 1.875188840 0.574337211 2.098875074 2.172795983
[66] -0.427499632 1.098867011 -0.500103225 -0.510400634 0.382004438
[71] 0.713564014 1.088631836 0.381256070 1.851770704 2.058940384
[76] 0.597017327 1.914805149 0.100880001 0.251013854 -1.001427426
[81] 0.967406760 -1.390758197 0.892304097 0.309140023 0.537778505
[86] 0.246276054 -0.773117269 0.734675331 0.988466613 -1.427911209
[91] -0.178238451 0.671793717 -0.361478146 0.317379756 -0.908538414
[96] -0.005703448 0.873436381 -0.895899837 1.403302419 1.471520161
> colMedians(tmp)
[1] 0.674770764 -0.088170254 -1.260533189 0.024321427 0.374758131
[6] 1.404130258 1.023349575 -0.313441508 -0.762725967 -0.575472523
[11] 0.171010213 -0.517091407 0.176753724 0.864248867 3.054453190
[16] -0.894373022 1.003653883 1.200439522 0.801696154 1.518937735
[21] 0.419405767 -0.381707032 -1.443081865 -2.045137222 0.774436533
[26] -0.578004255 0.441175359 -1.176329073 -0.765489711 0.461434631
[31] -0.460697707 -2.399968915 2.321675288 0.885702083 -0.678171910
[36] -0.642182580 -0.783834460 -0.315627818 0.885875036 1.201463844
[41] 1.410654825 -0.389889774 -0.045977780 0.941134635 -0.665040644
[46] 0.970632374 0.578498013 0.254240467 1.082884297 -0.289104967
[51] -0.138969640 0.614071493 0.517732077 -0.471027085 0.304705203
[56] -0.689777824 0.337540772 0.537433873 1.149376135 -0.724757284
[61] 0.345551042 1.875188840 0.574337211 2.098875074 2.172795983
[66] -0.427499632 1.098867011 -0.500103225 -0.510400634 0.382004438
[71] 0.713564014 1.088631836 0.381256070 1.851770704 2.058940384
[76] 0.597017327 1.914805149 0.100880001 0.251013854 -1.001427426
[81] 0.967406760 -1.390758197 0.892304097 0.309140023 0.537778505
[86] 0.246276054 -0.773117269 0.734675331 0.988466613 -1.427911209
[91] -0.178238451 0.671793717 -0.361478146 0.317379756 -0.908538414
[96] -0.005703448 0.873436381 -0.895899837 1.403302419 1.471520161
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.6747708 -0.08817025 -1.260533 0.02432143 0.3747581 1.40413 1.02335
[2,] 0.6747708 -0.08817025 -1.260533 0.02432143 0.3747581 1.40413 1.02335
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -0.3134415 -0.762726 -0.5754725 0.1710102 -0.5170914 0.1767537 0.8642489
[2,] -0.3134415 -0.762726 -0.5754725 0.1710102 -0.5170914 0.1767537 0.8642489
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22]
[1,] 3.054453 -0.894373 1.003654 1.20044 0.8016962 1.518938 0.4194058 -0.381707
[2,] 3.054453 -0.894373 1.003654 1.20044 0.8016962 1.518938 0.4194058 -0.381707
[,23] [,24] [,25] [,26] [,27] [,28] [,29]
[1,] -1.443082 -2.045137 0.7744365 -0.5780043 0.4411754 -1.176329 -0.7654897
[2,] -1.443082 -2.045137 0.7744365 -0.5780043 0.4411754 -1.176329 -0.7654897
[,30] [,31] [,32] [,33] [,34] [,35] [,36]
[1,] 0.4614346 -0.4606977 -2.399969 2.321675 0.8857021 -0.6781719 -0.6421826
[2,] 0.4614346 -0.4606977 -2.399969 2.321675 0.8857021 -0.6781719 -0.6421826
[,37] [,38] [,39] [,40] [,41] [,42] [,43]
[1,] -0.7838345 -0.3156278 0.885875 1.201464 1.410655 -0.3898898 -0.04597778
[2,] -0.7838345 -0.3156278 0.885875 1.201464 1.410655 -0.3898898 -0.04597778
[,44] [,45] [,46] [,47] [,48] [,49] [,50]
[1,] 0.9411346 -0.6650406 0.9706324 0.578498 0.2542405 1.082884 -0.289105
[2,] 0.9411346 -0.6650406 0.9706324 0.578498 0.2542405 1.082884 -0.289105
[,51] [,52] [,53] [,54] [,55] [,56] [,57]
[1,] -0.1389696 0.6140715 0.5177321 -0.4710271 0.3047052 -0.6897778 0.3375408
[2,] -0.1389696 0.6140715 0.5177321 -0.4710271 0.3047052 -0.6897778 0.3375408
[,58] [,59] [,60] [,61] [,62] [,63] [,64]
[1,] 0.5374339 1.149376 -0.7247573 0.345551 1.875189 0.5743372 2.098875
[2,] 0.5374339 1.149376 -0.7247573 0.345551 1.875189 0.5743372 2.098875
[,65] [,66] [,67] [,68] [,69] [,70] [,71]
[1,] 2.172796 -0.4274996 1.098867 -0.5001032 -0.5104006 0.3820044 0.713564
[2,] 2.172796 -0.4274996 1.098867 -0.5001032 -0.5104006 0.3820044 0.713564
[,72] [,73] [,74] [,75] [,76] [,77] [,78] [,79]
[1,] 1.088632 0.3812561 1.851771 2.05894 0.5970173 1.914805 0.10088 0.2510139
[2,] 1.088632 0.3812561 1.851771 2.05894 0.5970173 1.914805 0.10088 0.2510139
[,80] [,81] [,82] [,83] [,84] [,85] [,86]
[1,] -1.001427 0.9674068 -1.390758 0.8923041 0.30914 0.5377785 0.2462761
[2,] -1.001427 0.9674068 -1.390758 0.8923041 0.30914 0.5377785 0.2462761
[,87] [,88] [,89] [,90] [,91] [,92] [,93]
[1,] -0.7731173 0.7346753 0.9884666 -1.427911 -0.1782385 0.6717937 -0.3614781
[2,] -0.7731173 0.7346753 0.9884666 -1.427911 -0.1782385 0.6717937 -0.3614781
[,94] [,95] [,96] [,97] [,98] [,99] [,100]
[1,] 0.3173798 -0.9085384 -0.005703448 0.8734364 -0.8958998 1.403302 1.47152
[2,] 0.3173798 -0.9085384 -0.005703448 0.8734364 -0.8958998 1.403302 1.47152
>
>
> Max(tmp2)
[1] 2.524082
> Min(tmp2)
[1] -2.397402
> mean(tmp2)
[1] 0.07872181
> Sum(tmp2)
[1] 7.872181
> Var(tmp2)
[1] 0.9893729
>
> rowMeans(tmp2)
[1] 0.17822642 0.56445764 0.06604141 -0.01094965 0.02435388 2.52408174
[7] 0.71089876 -1.10931207 1.08426831 -0.58473893 0.32110675 -0.79312858
[13] -0.65435877 -1.20922207 0.49372633 -0.98357641 -1.53966856 -0.71135908
[19] 0.16735200 2.26436506 0.50826376 -0.36173604 -1.76416443 1.16089138
[25] -1.40899994 -0.86367648 -0.66194962 2.35693165 -0.10865671 1.53844908
[31] 0.28590669 -1.71901485 -0.64207856 0.41546142 -0.25340461 2.17650260
[37] -1.47893289 0.64098269 0.11739028 0.31496393 0.85887455 -0.61187060
[43] 0.48621450 -1.08762649 -0.30313896 1.05096384 1.15168112 0.16975631
[49] -1.23137096 -0.45312658 -0.60169137 -2.39740155 1.05328521 -0.01728862
[55] -0.19239349 1.65267716 -0.68656894 0.13715381 0.51697119 0.50183201
[61] -0.12831555 -0.29056827 0.64988919 1.02072938 -0.19844918 1.89445332
[67] 0.21724294 0.71666061 -0.34339626 -1.00966360 2.34676379 -1.09320488
[73] 0.64833199 -0.93092607 0.34010025 1.20336007 -0.52655485 -0.19516898
[79] 0.72858610 -0.91322594 0.53172673 0.48063168 -0.79975738 0.95202388
[85] 0.38432821 1.51084668 -0.74130267 0.44927925 1.33087240 0.50485493
[91] -1.34794315 -0.87830981 0.64541047 -1.14675038 0.30270754 -0.21046002
[97] 1.27986410 -0.04899451 -0.58372555 0.06760863
> rowSums(tmp2)
[1] 0.17822642 0.56445764 0.06604141 -0.01094965 0.02435388 2.52408174
[7] 0.71089876 -1.10931207 1.08426831 -0.58473893 0.32110675 -0.79312858
[13] -0.65435877 -1.20922207 0.49372633 -0.98357641 -1.53966856 -0.71135908
[19] 0.16735200 2.26436506 0.50826376 -0.36173604 -1.76416443 1.16089138
[25] -1.40899994 -0.86367648 -0.66194962 2.35693165 -0.10865671 1.53844908
[31] 0.28590669 -1.71901485 -0.64207856 0.41546142 -0.25340461 2.17650260
[37] -1.47893289 0.64098269 0.11739028 0.31496393 0.85887455 -0.61187060
[43] 0.48621450 -1.08762649 -0.30313896 1.05096384 1.15168112 0.16975631
[49] -1.23137096 -0.45312658 -0.60169137 -2.39740155 1.05328521 -0.01728862
[55] -0.19239349 1.65267716 -0.68656894 0.13715381 0.51697119 0.50183201
[61] -0.12831555 -0.29056827 0.64988919 1.02072938 -0.19844918 1.89445332
[67] 0.21724294 0.71666061 -0.34339626 -1.00966360 2.34676379 -1.09320488
[73] 0.64833199 -0.93092607 0.34010025 1.20336007 -0.52655485 -0.19516898
[79] 0.72858610 -0.91322594 0.53172673 0.48063168 -0.79975738 0.95202388
[85] 0.38432821 1.51084668 -0.74130267 0.44927925 1.33087240 0.50485493
[91] -1.34794315 -0.87830981 0.64541047 -1.14675038 0.30270754 -0.21046002
[97] 1.27986410 -0.04899451 -0.58372555 0.06760863
> 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] 0.17822642 0.56445764 0.06604141 -0.01094965 0.02435388 2.52408174
[7] 0.71089876 -1.10931207 1.08426831 -0.58473893 0.32110675 -0.79312858
[13] -0.65435877 -1.20922207 0.49372633 -0.98357641 -1.53966856 -0.71135908
[19] 0.16735200 2.26436506 0.50826376 -0.36173604 -1.76416443 1.16089138
[25] -1.40899994 -0.86367648 -0.66194962 2.35693165 -0.10865671 1.53844908
[31] 0.28590669 -1.71901485 -0.64207856 0.41546142 -0.25340461 2.17650260
[37] -1.47893289 0.64098269 0.11739028 0.31496393 0.85887455 -0.61187060
[43] 0.48621450 -1.08762649 -0.30313896 1.05096384 1.15168112 0.16975631
[49] -1.23137096 -0.45312658 -0.60169137 -2.39740155 1.05328521 -0.01728862
[55] -0.19239349 1.65267716 -0.68656894 0.13715381 0.51697119 0.50183201
[61] -0.12831555 -0.29056827 0.64988919 1.02072938 -0.19844918 1.89445332
[67] 0.21724294 0.71666061 -0.34339626 -1.00966360 2.34676379 -1.09320488
[73] 0.64833199 -0.93092607 0.34010025 1.20336007 -0.52655485 -0.19516898
[79] 0.72858610 -0.91322594 0.53172673 0.48063168 -0.79975738 0.95202388
[85] 0.38432821 1.51084668 -0.74130267 0.44927925 1.33087240 0.50485493
[91] -1.34794315 -0.87830981 0.64541047 -1.14675038 0.30270754 -0.21046002
[97] 1.27986410 -0.04899451 -0.58372555 0.06760863
> rowMin(tmp2)
[1] 0.17822642 0.56445764 0.06604141 -0.01094965 0.02435388 2.52408174
[7] 0.71089876 -1.10931207 1.08426831 -0.58473893 0.32110675 -0.79312858
[13] -0.65435877 -1.20922207 0.49372633 -0.98357641 -1.53966856 -0.71135908
[19] 0.16735200 2.26436506 0.50826376 -0.36173604 -1.76416443 1.16089138
[25] -1.40899994 -0.86367648 -0.66194962 2.35693165 -0.10865671 1.53844908
[31] 0.28590669 -1.71901485 -0.64207856 0.41546142 -0.25340461 2.17650260
[37] -1.47893289 0.64098269 0.11739028 0.31496393 0.85887455 -0.61187060
[43] 0.48621450 -1.08762649 -0.30313896 1.05096384 1.15168112 0.16975631
[49] -1.23137096 -0.45312658 -0.60169137 -2.39740155 1.05328521 -0.01728862
[55] -0.19239349 1.65267716 -0.68656894 0.13715381 0.51697119 0.50183201
[61] -0.12831555 -0.29056827 0.64988919 1.02072938 -0.19844918 1.89445332
[67] 0.21724294 0.71666061 -0.34339626 -1.00966360 2.34676379 -1.09320488
[73] 0.64833199 -0.93092607 0.34010025 1.20336007 -0.52655485 -0.19516898
[79] 0.72858610 -0.91322594 0.53172673 0.48063168 -0.79975738 0.95202388
[85] 0.38432821 1.51084668 -0.74130267 0.44927925 1.33087240 0.50485493
[91] -1.34794315 -0.87830981 0.64541047 -1.14675038 0.30270754 -0.21046002
[97] 1.27986410 -0.04899451 -0.58372555 0.06760863
>
> colMeans(tmp2)
[1] 0.07872181
> colSums(tmp2)
[1] 7.872181
> colVars(tmp2)
[1] 0.9893729
> colSd(tmp2)
[1] 0.9946723
> colMax(tmp2)
[1] 2.524082
> colMin(tmp2)
[1] -2.397402
> colMedians(tmp2)
[1] 0.09249946
> colRanges(tmp2)
[,1]
[1,] -2.397402
[2,] 2.524082
>
> 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] -3.88130285 -3.49012279 -4.34288888 3.24842393 -0.08460884 -5.68011676
[7] -0.13876197 -1.39581933 -7.63549625 -0.12252003
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.8597817
[2,] -1.0734976
[3,] -0.3729861
[4,] 0.1410766
[5,] 0.9303040
>
> rowApply(tmp,sum)
[1] -2.088322 -5.384675 -2.152107 3.321245 -4.076751 -3.276921 -1.566785
[8] -7.627211 1.661778 -2.333465
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 9 7 3 1 6 5 2 4 5 10
[2,] 2 9 6 3 1 9 6 3 6 5
[3,] 6 8 10 8 9 2 3 7 1 2
[4,] 4 4 4 10 4 6 9 9 9 8
[5,] 3 2 9 4 2 10 1 10 8 7
[6,] 8 3 1 2 7 7 4 1 10 4
[7,] 7 5 8 5 3 3 10 8 4 3
[8,] 10 1 2 6 8 8 8 5 2 9
[9,] 5 6 5 7 5 1 5 2 3 1
[10,] 1 10 7 9 10 4 7 6 7 6
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -2.229326194 0.112503796 -2.662907496 1.357549707 -1.290332828
[6] 0.009847135 -0.355632105 -1.166661598 -0.688894404 4.059855615
[11] 0.121084597 -1.243397835 -3.049827395 3.421038929 2.239659578
[16] 0.092315169 -1.224887826 -0.256815623 3.289531754 2.846802592
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.1675249
[2,] -0.7396935
[3,] -0.5316364
[4,] -0.1011897
[5,] 0.3107183
>
> rowApply(tmp,sum)
[1] -1.2851995 3.5157860 0.9836294 -3.2099572 3.3772469
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 10 11 3 10 3
[2,] 12 2 14 13 16
[3,] 16 4 1 2 14
[4,] 20 6 6 20 2
[5,] 11 1 19 5 13
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.1011897 0.1433916 0.7218569 1.33043039 -0.03528983 0.76417976
[2,] 0.3107183 -1.3551630 -0.3528387 -0.06695768 -2.57999865 -0.06237868
[3,] -1.1675249 0.5341933 -2.3202238 -0.49684192 1.91795078 -0.88787657
[4,] -0.5316364 0.1004322 -1.3175780 1.45102206 -0.88744394 0.78485495
[5,] -0.7396935 0.6896497 0.6058761 -0.86010315 0.29444881 -0.58893232
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] -1.5934484 -1.156838174 -1.5309027 0.3065560 -0.201883658 0.5601955
[2,] 1.0865499 0.007387426 1.5037346 0.4613180 0.004949218 0.5044721
[3,] -0.2116934 -0.935213380 -1.7080345 2.0150912 1.364553217 0.2504927
[4,] -1.2458220 0.006493462 0.7596893 1.0715483 -0.570865925 -0.1884808
[5,] 1.6087817 0.911509069 0.2866187 0.2053422 -0.475668254 -2.3700773
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.9412099 0.3098331 -0.5311984 -0.52463608 1.1985943 -0.8328086
[2,] -0.5265359 0.3792244 -0.3079633 1.21817654 0.4781215 0.1252734
[3,] -0.4524106 0.8707949 1.3160124 -0.12272644 -0.2391662 -0.0091864
[4,] -1.2405845 0.9885383 -0.6585853 -0.53193042 -1.9386222 0.3109744
[5,] 0.1109134 0.8726483 2.4213942 0.05343157 -0.7238152 0.1489316
[,19] [,20]
[1,] -0.1439741 0.97314226
[2,] 0.3206824 2.36701414
[3,] 1.2051149 0.06032411
[4,] 1.2377026 -0.80966311
[5,] 0.6700060 0.25598519
>
>
> 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 : 648 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 : 560 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 -0.4360155 0.1522901 0.4950431 0.9287277 -1.388014 2.045187 0.7959823
col8 col9 col10 col11 col12 col13 col14
row1 -0.04066154 -0.4765888 0.9911629 -0.6563276 -0.6624855 1.043963 0.3553994
col15 col16 col17 col18 col19 col20
row1 -0.5384657 -0.2859037 -0.9282345 -1.362532 -0.4412858 -1.279357
> tmp[,"col10"]
col10
row1 0.99116293
row2 0.24351418
row3 0.18338380
row4 0.56611293
row5 0.02805106
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -0.4360155 0.1522901 0.4950431 0.9287277 -1.3880139 2.045187 0.7959823
row5 -1.3392825 0.2100977 0.1102654 0.1453685 -0.9877764 -0.964579 -0.8411413
col8 col9 col10 col11 col12 col13
row1 -0.04066154 -0.4765888 0.99116293 -0.6563276 -0.6624855 1.043963
row5 1.23675785 -0.0635404 0.02805106 2.2571943 0.8843684 1.604915
col14 col15 col16 col17 col18 col19
row1 0.3553994 -0.5384657 -0.2859037 -0.9282345 -1.3625324 -0.4412858
row5 -1.4100672 0.1681059 1.7197111 -1.4802382 -0.4389703 -0.4760915
col20
row1 -1.2793572
row5 0.9234556
> tmp[,c("col6","col20")]
col6 col20
row1 2.0451874 -1.2793572
row2 -0.3388833 0.2394536
row3 -0.6762119 0.5419491
row4 -0.4132941 1.1281489
row5 -0.9645790 0.9234556
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 2.045187 -1.2793572
row5 -0.964579 0.9234556
>
>
>
>
> 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 48.68019 48.88106 50.69699 50.00201 49.52609 104.3099 51.47515 48.84717
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.57361 50.7873 49.39321 49.04366 48.76516 49.00531 48.35434 49.89369
col17 col18 col19 col20
row1 50.41275 50.38172 49.45382 105.7581
> tmp[,"col10"]
col10
row1 50.78730
row2 30.07044
row3 28.98258
row4 30.06817
row5 50.25278
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 48.68019 48.88106 50.69699 50.00201 49.52609 104.3099 51.47515 48.84717
row5 50.80169 50.62691 51.45183 50.00063 50.63606 103.6394 47.55375 49.58850
col9 col10 col11 col12 col13 col14 col15 col16
row1 50.57361 50.78730 49.39321 49.04366 48.76516 49.00531 48.35434 49.89369
row5 49.49799 50.25278 51.16473 51.03742 52.31132 50.87539 50.31252 50.47890
col17 col18 col19 col20
row1 50.41275 50.38172 49.45382 105.7581
row5 50.71835 51.97183 49.59391 104.1741
> tmp[,c("col6","col20")]
col6 col20
row1 104.30988 105.75806
row2 74.29005 76.13845
row3 73.07081 75.55523
row4 74.66990 75.62629
row5 103.63937 104.17410
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.3099 105.7581
row5 103.6394 104.1741
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.3099 105.7581
row5 103.6394 104.1741
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.2077168
[2,] -1.1292994
[3,] -0.2775753
[4,] -0.6787059
[5,] 1.4879395
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.4777959 -0.2361998
[2,] -0.4200971 0.7388871
[3,] 2.2215576 -1.0011976
[4,] -0.7007897 -0.9544018
[5,] 0.0621173 1.0534631
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 0.1147808 -1.2679994
[2,] 1.0302075 -0.2149434
[3,] 0.8374626 0.4103501
[4,] 0.4623167 -0.8393465
[5,] 0.2156598 0.1381774
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 0.1147808
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 0.1147808
[2,] 1.0302075
>
>
>
> 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 1.5045252 -0.2494987 -0.4053720 1.0312804 -0.1583072 1.958107 -1.5395897
row1 -0.4393356 -0.1035991 0.6573219 0.4102111 0.3614844 1.566607 -0.7955661
[,8] [,9] [,10] [,11] [,12] [,13]
row3 0.1728204 -0.4967824 2.1029909 1.1715529 0.2063601 -0.74169391
row1 0.4641361 -0.4140692 -0.8002958 0.8394585 -0.1128320 0.08990406
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 -1.0097665 -0.8177532 -0.8302894 0.2610412 0.1231769 0.6773805 0.4648956
row1 -0.7166383 -1.3433604 0.7093545 0.9198823 0.1499701 -1.9437752 -0.1130704
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 -1.565883 -0.8853593 1.511202 1.322821 1.492151 -0.6334687 0.3114497
[,8] [,9] [,10]
row2 -1.14347 -1.641521 0.669347
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -2.080869 -0.2459177 -0.5370843 -0.1861035 -1.113653 0.1783517 0.3632135
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 0.9313776 0.03308942 -0.8790677 -0.7363946 -0.2233771 -0.5410624 -1.276512
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.04846801 0.2746138 1.572959 -1.112148 0.4501503 -0.2802772
>
>
> 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: 0x5689b7fab320>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM4b87179fa3836"
[2] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM4b8714668c360"
[3] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM4b8714fb420f3"
[4] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM4b87177886d49"
[5] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM4b8711b4fde97"
[6] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM4b8713c85d320"
[7] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM4b87171afe727"
[8] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM4b8714b41c977"
[9] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM4b871480a3ab0"
[10] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM4b87119413e45"
[11] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM4b87130ee6e2f"
[12] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM4b87132a3f6eb"
[13] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM4b8712289e3c4"
[14] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM4b871411a9e08"
[15] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM4b87142ff810a"
>
>
> ### 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: 0x5689b86306f0>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x5689b86306f0>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x5689b86306f0>
> rowMedians(tmp)
[1] 0.1583055485 0.2327050748 0.1723834277 -0.0925766626 0.2645568437
[6] 0.1528075309 -0.8369742938 0.4723795338 0.3403208391 -0.2941177584
[11] 0.0880765814 -0.5627862971 -0.4949437659 0.4886455305 -0.0486975691
[16] 0.3429215643 0.5001981654 -0.6091833521 -0.2090051140 0.1194783067
[21] -0.4716415833 0.3225697485 0.0355475450 -0.3586134913 -0.5424235550
[26] -0.0484339299 0.0704813776 -0.2858887780 0.2370029302 -0.1868254350
[31] -0.3486340614 0.0877107421 -0.1760328682 0.1466316275 -0.0913970341
[36] -0.0705202239 -0.5351692527 -0.2479144828 0.1411225614 0.5812563819
[41] 0.1652933822 0.0937202520 -0.3221834950 -0.0568539836 -0.2424429423
[46] 0.1816410263 0.2030423722 -0.1930200645 -0.1410416410 -0.0669630254
[51] -0.2968047559 0.0262702762 0.4613995169 -0.2492300029 -0.5194104999
[56] 0.0182769960 -0.1261771875 0.1013013885 0.2961196209 -0.2315773578
[61] 0.2517167870 0.1307266427 0.3929088216 0.1100751811 -0.2569672848
[66] -0.2069418136 -0.0571040175 0.5845994685 -0.0249207259 -0.2849148904
[71] 0.7662795243 -0.1118529289 0.0674182807 -0.6330556099 0.0325422267
[76] 0.1231020934 0.6937166333 0.3259681826 -0.2650275241 -0.0724537325
[81] -0.3234665462 -0.4140955773 -0.1303024520 -0.1004523775 0.1941676722
[86] -0.1069844716 -0.1839936277 -0.0145298665 -0.0153781714 0.1955570008
[91] -0.2716695107 -0.1592627432 -0.0798497328 -0.3170774374 0.3233698697
[96] -0.7147192984 -0.2153582699 -0.0030154025 -0.4389061556 0.1060913735
[101] -0.1453720715 -0.1540101723 -0.1509207281 -0.6229544841 0.1916849511
[106] -0.1592803307 0.4192981713 -0.1404077368 -0.3992434684 0.3282230239
[111] 0.0294758744 0.1035038197 0.0543663040 -0.4572393458 -0.1522716980
[116] -0.2020921827 -0.2094079452 0.3304481415 -0.3141778209 -0.0402685377
[121] 0.2609033337 0.2231993884 -0.5137662220 -0.1633294725 0.7893588000
[126] 0.3096246792 -0.2296629179 -0.2994747827 0.1374176753 -0.2900877518
[131] -0.4056165182 -0.4199662600 -0.0439050094 -0.1319338867 -0.0682344957
[136] -0.0840365081 0.3715790200 0.3083457771 0.0295531483 -0.2582106256
[141] 0.0720478438 -0.0001295606 -0.5418689029 -0.5386251189 -0.0850536318
[146] -0.1364641369 -0.0441612917 -0.3668101214 -0.0800092596 -0.2395015354
[151] -0.0053546678 0.2408598087 -0.0037092651 0.2765198366 0.0484233805
[156] -0.0404148172 0.1588132861 -0.2609913086 0.1246519097 -0.2871014002
[161] 0.2341162940 0.0394049860 0.3772960414 -0.4983545730 0.4170279925
[166] 0.2739649529 0.1203743659 -0.2851729883 -0.1210878114 0.1005282625
[171] 0.0149174479 -0.4401555367 0.3955452550 0.6148992423 0.1720115291
[176] -0.1943331624 -0.9086364276 0.5668386987 -0.1947576600 -0.3868973529
[181] -0.4652571147 0.2047095317 -0.2651387817 -0.1889498927 0.2687641633
[186] 0.0267240474 0.3546194455 0.1455744657 -0.2043094021 -0.4161489200
[191] 0.3582238234 -0.2243596478 -0.1370613968 0.0244539666 -0.0653020876
[196] 0.2538834884 0.5151162215 -0.0029551458 -0.3393691938 -0.2323340509
[201] 0.0020251945 -0.7832184467 -0.4704869974 0.3245076420 0.2787656790
[206] -0.2845668368 -0.2672188701 -0.2063069460 -0.3532418286 0.1311943479
[211] 0.2609756350 0.0409720789 -0.5628917490 -0.0793023233 -0.3159967738
[216] 0.1377307448 0.2330992704 0.1625046007 -0.1299989222 0.3249300104
[221] -0.0695367903 -0.1444381347 0.3214261584 -0.0887790175 -0.5801705630
[226] 0.0694045715 -0.2757684259 -0.0655081376 0.1171017688 -0.3082158283
>
> proc.time()
user system elapsed
1.272 0.676 1.937
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: 0x5e428b4091c0>
> .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: 0x5e428b4091c0>
> .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: 0x5e428b4091c0>
> .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: 0x5e428b4091c0>
> 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: 0x5e428b6ec120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e428b6ec120>
> .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: 0x5e428b6ec120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e428b6ec120>
> .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: 0x5e428b6ec120>
> 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: 0x5e428a3a04a0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e428a3a04a0>
> .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: 0x5e428a3a04a0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5e428a3a04a0>
> .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: 0x5e428a3a04a0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x5e428a3a04a0>
> .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: 0x5e428a3a04a0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x5e428a3a04a0>
> .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: 0x5e428a3a04a0>
> 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: 0x5e428a43c390>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x5e428a43c390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e428a43c390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e428a43c390>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile4b9842428eb28" "BufferedMatrixFile4b984955cab0"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile4b9842428eb28" "BufferedMatrixFile4b984955cab0"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e428a3333d0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e428a3333d0>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5e428a3333d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5e428a3333d0>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x5e428a3333d0>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x5e428a3333d0>
> .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: 0x5e428be68fa0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5e428be68fa0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5e428be68fa0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x5e428be68fa0>
> 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: 0x5e428c3e25d0>
> .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: 0x5e428c3e25d0>
> rm(P)
>
> proc.time()
user system elapsed
0.236 0.052 0.276
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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Type 'license()' or 'licence()' for distribution details.
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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
0.254 0.053 0.296