Ben Bolstad
| Snapshot Date: 2025-09-22 13:40 -0400 (Mon, 22 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_21 |
| git_last_commit: aa9e634 |
| git_last_commit_date: 2025-04-15 09:39:39 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-25 11:38 -0400 (Thu, 25 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
| 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 252/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.72.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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: 1.72.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BufferedMatrix_1.72.0.tar.gz |
| StartedAt: 2025-09-24 21:52:41 -0400 (Wed, 24 Sep 2025) |
| EndedAt: 2025-09-24 21:53:06 -0400 (Wed, 24 Sep 2025) |
| EllapsedTime: 25.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BufferedMatrix_1.72.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.72.0’
* 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-3.21-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.72.0’
** 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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-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-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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 4.5.1 (2025-06-13) -- "Great Square Root"
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
0.244 0.050 0.283
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
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-3.21-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 478417 25.6 1047105 56 639600 34.2
Vcells 885231 6.8 8388608 64 2081598 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] "Wed Sep 24 21:52:56 2025"
> 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] "Wed Sep 24 21:52:56 2025"
>
>
> 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: 0x581c4517ead0>
>
>
>
> 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] "Wed Sep 24 21:52:57 2025"
> 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] "Wed Sep 24 21:52:57 2025"
>
> ColMode(tmp2)
<pointer: 0x581c4517ead0>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.1837732 -0.1729032 2.153346 1.1244005
[2,] -0.7209000 0.2401661 1.108860 0.8627606
[3,] -0.8194452 -0.1952508 0.439297 -0.5011007
[4,] 0.7481430 -0.2321267 1.681271 1.0120550
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.1837732 0.1729032 2.153346 1.1244005
[2,] 0.7209000 0.2401661 1.108860 0.8627606
[3,] 0.8194452 0.1952508 0.439297 0.5011007
[4,] 0.7481430 0.2321267 1.681271 1.0120550
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.0091844 0.4158163 1.4674282 1.0603775
[2,] 0.8490583 0.4900675 1.0530244 0.9288491
[3,] 0.9052321 0.4418720 0.6627948 0.7078847
[4,] 0.8649526 0.4817953 1.2966384 1.0060094
>
> 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-3.21-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 225.27562 29.33107 41.82763 36.72818
[2,] 34.21148 30.14084 36.63910 35.15125
[3,] 34.87177 29.61397 32.06725 32.57995
[4,] 34.39767 30.05008 39.64766 36.07215
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x581c45dba960>
> exp(tmp5)
<pointer: 0x581c45dba960>
> log(tmp5,2)
<pointer: 0x581c45dba960>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 468.8817
> Min(tmp5)
[1] 53.69848
> mean(tmp5)
[1] 73.06115
> Sum(tmp5)
[1] 14612.23
> Var(tmp5)
[1] 864.2632
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 92.21168 71.34766 68.81247 71.31663 69.38564 71.98472 69.01841 73.05172
[9] 71.45265 72.02996
> rowSums(tmp5)
[1] 1844.234 1426.953 1376.249 1426.333 1387.713 1439.694 1380.368 1461.034
[9] 1429.053 1440.599
> rowVars(tmp5)
[1] 7927.19219 46.83729 34.25166 91.76813 57.54208 88.50827
[7] 101.37199 122.66692 83.08758 50.96671
> rowSd(tmp5)
[1] 89.034781 6.843778 5.852491 9.579568 7.585650 9.407884 10.068366
[8] 11.075510 9.115239 7.139097
> rowMax(tmp5)
[1] 468.88168 86.57996 77.94664 86.53988 86.75179 92.35473 91.48539
[8] 88.97882 88.34630 85.45040
> rowMin(tmp5)
[1] 59.48084 59.02423 58.05905 54.40445 54.73314 56.44571 53.69848 56.11213
[9] 55.47702 60.34932
>
> colMeans(tmp5)
[1] 109.46322 67.62572 72.35280 75.94091 70.00792 68.63009 73.29654
[8] 68.19124 71.14844 71.57751 70.29612 72.10712 67.95089 72.97951
[15] 68.39521 72.44916 75.87548 71.58070 69.78778 71.56674
> colSums(tmp5)
[1] 1094.6322 676.2572 723.5280 759.4091 700.0792 686.3009 732.9654
[8] 681.9124 711.4844 715.7751 702.9612 721.0712 679.5089 729.7951
[15] 683.9521 724.4916 758.7548 715.8070 697.8778 715.6674
> colVars(tmp5)
[1] 15992.19134 48.19718 110.55934 40.25358 80.36920 45.11844
[7] 87.27804 116.17179 30.96824 149.54785 74.13815 51.06820
[13] 74.93272 88.39752 51.55860 101.99879 68.15475 70.47087
[19] 93.30478 66.34108
> colSd(tmp5)
[1] 126.460236 6.942419 10.514720 6.344571 8.964887 6.717026
[7] 9.342272 10.778302 5.564911 12.228976 8.610352 7.146202
[13] 8.656369 9.401995 7.180432 10.099445 8.255589 8.394693
[19] 9.659440 8.145004
> colMax(tmp5)
[1] 468.88168 80.39454 87.05873 86.38645 84.46205 77.64767 86.73966
[8] 92.35473 79.97611 91.48539 82.36893 83.79447 84.17304 88.34630
[15] 80.52443 85.39841 86.75179 86.53988 88.43770 86.57996
> colMin(tmp5)
[1] 55.47702 60.63209 55.82185 67.81089 58.17706 59.75453 59.79488 57.01789
[9] 60.99922 57.93054 56.44571 61.58426 53.69848 59.11333 57.59058 54.40445
[17] 63.72558 56.90669 54.73314 60.11583
>
>
> ### 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] 92.21168 71.34766 68.81247 71.31663 69.38564 71.98472 NA 73.05172
[9] 71.45265 72.02996
> rowSums(tmp5)
[1] 1844.234 1426.953 1376.249 1426.333 1387.713 1439.694 NA 1461.034
[9] 1429.053 1440.599
> rowVars(tmp5)
[1] 7927.19219 46.83729 34.25166 91.76813 57.54208 88.50827
[7] 105.20604 122.66692 83.08758 50.96671
> rowSd(tmp5)
[1] 89.034781 6.843778 5.852491 9.579568 7.585650 9.407884 10.257000
[8] 11.075510 9.115239 7.139097
> rowMax(tmp5)
[1] 468.88168 86.57996 77.94664 86.53988 86.75179 92.35473 NA
[8] 88.97882 88.34630 85.45040
> rowMin(tmp5)
[1] 59.48084 59.02423 58.05905 54.40445 54.73314 56.44571 NA 56.11213
[9] 55.47702 60.34932
>
> colMeans(tmp5)
[1] 109.46322 67.62572 72.35280 75.94091 70.00792 68.63009 73.29654
[8] 68.19124 71.14844 71.57751 70.29612 72.10712 67.95089 72.97951
[15] 68.39521 72.44916 75.87548 71.58070 NA 71.56674
> colSums(tmp5)
[1] 1094.6322 676.2572 723.5280 759.4091 700.0792 686.3009 732.9654
[8] 681.9124 711.4844 715.7751 702.9612 721.0712 679.5089 729.7951
[15] 683.9521 724.4916 758.7548 715.8070 NA 715.6674
> colVars(tmp5)
[1] 15992.19134 48.19718 110.55934 40.25358 80.36920 45.11844
[7] 87.27804 116.17179 30.96824 149.54785 74.13815 51.06820
[13] 74.93272 88.39752 51.55860 101.99879 68.15475 70.47087
[19] NA 66.34108
> colSd(tmp5)
[1] 126.460236 6.942419 10.514720 6.344571 8.964887 6.717026
[7] 9.342272 10.778302 5.564911 12.228976 8.610352 7.146202
[13] 8.656369 9.401995 7.180432 10.099445 8.255589 8.394693
[19] NA 8.145004
> colMax(tmp5)
[1] 468.88168 80.39454 87.05873 86.38645 84.46205 77.64767 86.73966
[8] 92.35473 79.97611 91.48539 82.36893 83.79447 84.17304 88.34630
[15] 80.52443 85.39841 86.75179 86.53988 NA 86.57996
> colMin(tmp5)
[1] 55.47702 60.63209 55.82185 67.81089 58.17706 59.75453 59.79488 57.01789
[9] 60.99922 57.93054 56.44571 61.58426 53.69848 59.11333 57.59058 54.40445
[17] 63.72558 56.90669 NA 60.11583
>
> Max(tmp5,na.rm=TRUE)
[1] 468.8817
> Min(tmp5,na.rm=TRUE)
[1] 53.69848
> mean(tmp5,na.rm=TRUE)
[1] 73.10933
> Sum(tmp5,na.rm=TRUE)
[1] 14548.76
> Var(tmp5,na.rm=TRUE)
[1] 868.1616
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.21168 71.34766 68.81247 71.31663 69.38564 71.98472 69.31023 73.05172
[9] 71.45265 72.02996
> rowSums(tmp5,na.rm=TRUE)
[1] 1844.234 1426.953 1376.249 1426.333 1387.713 1439.694 1316.894 1461.034
[9] 1429.053 1440.599
> rowVars(tmp5,na.rm=TRUE)
[1] 7927.19219 46.83729 34.25166 91.76813 57.54208 88.50827
[7] 105.20604 122.66692 83.08758 50.96671
> rowSd(tmp5,na.rm=TRUE)
[1] 89.034781 6.843778 5.852491 9.579568 7.585650 9.407884 10.257000
[8] 11.075510 9.115239 7.139097
> rowMax(tmp5,na.rm=TRUE)
[1] 468.88168 86.57996 77.94664 86.53988 86.75179 92.35473 91.48539
[8] 88.97882 88.34630 85.45040
> rowMin(tmp5,na.rm=TRUE)
[1] 59.48084 59.02423 58.05905 54.40445 54.73314 56.44571 53.69848 56.11213
[9] 55.47702 60.34932
>
> colMeans(tmp5,na.rm=TRUE)
[1] 109.46322 67.62572 72.35280 75.94091 70.00792 68.63009 73.29654
[8] 68.19124 71.14844 71.57751 70.29612 72.10712 67.95089 72.97951
[15] 68.39521 72.44916 75.87548 71.58070 70.48932 71.56674
> colSums(tmp5,na.rm=TRUE)
[1] 1094.6322 676.2572 723.5280 759.4091 700.0792 686.3009 732.9654
[8] 681.9124 711.4844 715.7751 702.9612 721.0712 679.5089 729.7951
[15] 683.9521 724.4916 758.7548 715.8070 634.4038 715.6674
> colVars(tmp5,na.rm=TRUE)
[1] 15992.19134 48.19718 110.55934 40.25358 80.36920 45.11844
[7] 87.27804 116.17179 30.96824 149.54785 74.13815 51.06820
[13] 74.93272 88.39752 51.55860 101.99879 68.15475 70.47087
[19] 99.43115 66.34108
> colSd(tmp5,na.rm=TRUE)
[1] 126.460236 6.942419 10.514720 6.344571 8.964887 6.717026
[7] 9.342272 10.778302 5.564911 12.228976 8.610352 7.146202
[13] 8.656369 9.401995 7.180432 10.099445 8.255589 8.394693
[19] 9.971517 8.145004
> colMax(tmp5,na.rm=TRUE)
[1] 468.88168 80.39454 87.05873 86.38645 84.46205 77.64767 86.73966
[8] 92.35473 79.97611 91.48539 82.36893 83.79447 84.17304 88.34630
[15] 80.52443 85.39841 86.75179 86.53988 88.43770 86.57996
> colMin(tmp5,na.rm=TRUE)
[1] 55.47702 60.63209 55.82185 67.81089 58.17706 59.75453 59.79488 57.01789
[9] 60.99922 57.93054 56.44571 61.58426 53.69848 59.11333 57.59058 54.40445
[17] 63.72558 56.90669 54.73314 60.11583
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.21168 71.34766 68.81247 71.31663 69.38564 71.98472 NaN 73.05172
[9] 71.45265 72.02996
> rowSums(tmp5,na.rm=TRUE)
[1] 1844.234 1426.953 1376.249 1426.333 1387.713 1439.694 0.000 1461.034
[9] 1429.053 1440.599
> rowVars(tmp5,na.rm=TRUE)
[1] 7927.19219 46.83729 34.25166 91.76813 57.54208 88.50827
[7] NA 122.66692 83.08758 50.96671
> rowSd(tmp5,na.rm=TRUE)
[1] 89.034781 6.843778 5.852491 9.579568 7.585650 9.407884 NA
[8] 11.075510 9.115239 7.139097
> rowMax(tmp5,na.rm=TRUE)
[1] 468.88168 86.57996 77.94664 86.53988 86.75179 92.35473 NA
[8] 88.97882 88.34630 85.45040
> rowMin(tmp5,na.rm=TRUE)
[1] 59.48084 59.02423 58.05905 54.40445 54.73314 56.44571 NA 56.11213
[9] 55.47702 60.34932
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 114.28373 68.40279 74.18957 75.55135 68.66996 69.46543 72.41043
[8] 68.09120 70.76824 69.36552 70.36652 73.27633 69.53449 72.91384
[15] 69.59572 73.51340 77.22547 70.96194 NaN 71.13171
> colSums(tmp5,na.rm=TRUE)
[1] 1028.5535 615.6251 667.7061 679.9621 618.0296 625.1889 651.6939
[8] 612.8208 636.9142 624.2897 633.2987 659.4870 625.8104 656.2245
[15] 626.3615 661.6206 695.0292 638.6574 0.0000 640.1854
> colVars(tmp5,na.rm=TRUE)
[1] 17729.79531 47.42864 86.42478 43.57801 70.27644 42.90799
[7] 89.35434 130.58067 33.21310 113.19634 83.34967 42.07246
[13] 56.08665 99.39868 41.78952 102.00694 56.17131 74.97252
[19] NA 72.50466
> colSd(tmp5,na.rm=TRUE)
[1] 133.153277 6.886845 9.296493 6.601364 8.383104 6.550419
[7] 9.452742 11.427190 5.763081 10.639377 9.129604 6.486329
[13] 7.489102 9.969889 6.464482 10.099848 7.494752 8.658667
[19] NA 8.514967
> colMax(tmp5,na.rm=TRUE)
[1] 468.88168 80.39454 87.05873 86.38645 84.46205 77.64767 86.73966
[8] 92.35473 79.97611 88.97882 82.36893 83.79447 84.17304 88.34630
[15] 80.52443 85.39841 86.75179 86.53988 -Inf 86.57996
> colMin(tmp5,na.rm=TRUE)
[1] 55.47702 61.04877 56.11213 67.81089 58.17706 59.75453 59.79488 57.01789
[9] 60.99922 57.93054 56.44571 65.59674 60.46590 59.11333 60.34510 54.40445
[17] 67.18323 56.90669 Inf 60.11583
>
>
>
>
> 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] 212.8453 163.5349 297.7904 192.6186 245.7317 196.7129 134.2331 178.0544
[9] 249.7911 166.1551
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 212.8453 163.5349 297.7904 192.6186 245.7317 196.7129 134.2331 178.0544
[9] 249.7911 166.1551
>
>
>
> 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] -8.526513e-14 5.684342e-14 8.526513e-14 -5.684342e-14 2.842171e-14
[6] 8.526513e-14 1.563194e-13 8.526513e-14 1.136868e-13 2.131628e-14
[11] 5.684342e-14 -5.684342e-14 0.000000e+00 7.105427e-14 -1.136868e-13
[16] 0.000000e+00 5.684342e-14 5.684342e-14 0.000000e+00 0.000000e+00
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
3 18
5 10
9 19
8 16
4 16
4 8
2 12
9 14
2 3
8 14
8 8
10 7
10 1
4 2
8 3
9 8
2 9
7 18
9 11
9 16
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] 2.275542
> Min(tmp)
[1] -1.895043
> mean(tmp)
[1] 0.07307407
> Sum(tmp)
[1] 7.307407
> Var(tmp)
[1] 0.7957751
>
> rowMeans(tmp)
[1] 0.07307407
> rowSums(tmp)
[1] 7.307407
> rowVars(tmp)
[1] 0.7957751
> rowSd(tmp)
[1] 0.8920623
> rowMax(tmp)
[1] 2.275542
> rowMin(tmp)
[1] -1.895043
>
> colMeans(tmp)
[1] 0.665409686 1.088818726 1.243414626 0.803531133 -0.000698263
[6] -0.834704881 0.761433472 -1.578063908 0.127059218 0.200173507
[11] -0.364529983 -0.499905370 1.149904709 -0.329347352 1.103820277
[16] 0.347414136 -0.433689168 -0.342538472 0.194236102 0.753166806
[21] -1.490395540 -1.061591063 0.115948301 0.122238292 0.012600256
[26] 1.917545602 0.366278067 0.738799805 0.328381837 1.224323578
[31] 0.520245466 0.694093054 1.414438109 1.279585906 0.378594294
[36] 0.774978734 -1.082392630 0.008689405 1.071237232 0.063567511
[41] -1.895042857 -0.739346060 2.013216964 -1.314931194 -0.283739396
[46] -0.372752870 -0.412826842 -0.159312463 -0.127335663 -1.164570915
[51] 0.425077343 0.454675201 -0.403478381 -0.504487918 -0.053677979
[56] 0.739830381 -1.130567784 -0.069717679 -1.056333471 -0.544869060
[61] 2.275542119 0.559483937 1.430060430 -1.115133306 0.796833579
[66] 0.647732862 0.874890727 1.697912901 -0.141471235 -0.466059205
[71] 0.665296622 -0.239843407 0.284195631 0.473626512 0.903573678
[76] -0.892063358 0.569196401 -1.671882517 1.092067800 -0.925160786
[81] -0.158013492 1.390376882 -0.680171199 -1.420587175 -0.548727495
[86] -0.897782061 0.990272258 -0.888357406 0.129042914 0.225755491
[91] -0.799569813 0.263117022 0.360612964 0.148651062 1.412463379
[96] -0.907165816 -0.528513732 -1.307370272 -0.433195019 -0.714111720
> colSums(tmp)
[1] 0.665409686 1.088818726 1.243414626 0.803531133 -0.000698263
[6] -0.834704881 0.761433472 -1.578063908 0.127059218 0.200173507
[11] -0.364529983 -0.499905370 1.149904709 -0.329347352 1.103820277
[16] 0.347414136 -0.433689168 -0.342538472 0.194236102 0.753166806
[21] -1.490395540 -1.061591063 0.115948301 0.122238292 0.012600256
[26] 1.917545602 0.366278067 0.738799805 0.328381837 1.224323578
[31] 0.520245466 0.694093054 1.414438109 1.279585906 0.378594294
[36] 0.774978734 -1.082392630 0.008689405 1.071237232 0.063567511
[41] -1.895042857 -0.739346060 2.013216964 -1.314931194 -0.283739396
[46] -0.372752870 -0.412826842 -0.159312463 -0.127335663 -1.164570915
[51] 0.425077343 0.454675201 -0.403478381 -0.504487918 -0.053677979
[56] 0.739830381 -1.130567784 -0.069717679 -1.056333471 -0.544869060
[61] 2.275542119 0.559483937 1.430060430 -1.115133306 0.796833579
[66] 0.647732862 0.874890727 1.697912901 -0.141471235 -0.466059205
[71] 0.665296622 -0.239843407 0.284195631 0.473626512 0.903573678
[76] -0.892063358 0.569196401 -1.671882517 1.092067800 -0.925160786
[81] -0.158013492 1.390376882 -0.680171199 -1.420587175 -0.548727495
[86] -0.897782061 0.990272258 -0.888357406 0.129042914 0.225755491
[91] -0.799569813 0.263117022 0.360612964 0.148651062 1.412463379
[96] -0.907165816 -0.528513732 -1.307370272 -0.433195019 -0.714111720
> 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] 0.665409686 1.088818726 1.243414626 0.803531133 -0.000698263
[6] -0.834704881 0.761433472 -1.578063908 0.127059218 0.200173507
[11] -0.364529983 -0.499905370 1.149904709 -0.329347352 1.103820277
[16] 0.347414136 -0.433689168 -0.342538472 0.194236102 0.753166806
[21] -1.490395540 -1.061591063 0.115948301 0.122238292 0.012600256
[26] 1.917545602 0.366278067 0.738799805 0.328381837 1.224323578
[31] 0.520245466 0.694093054 1.414438109 1.279585906 0.378594294
[36] 0.774978734 -1.082392630 0.008689405 1.071237232 0.063567511
[41] -1.895042857 -0.739346060 2.013216964 -1.314931194 -0.283739396
[46] -0.372752870 -0.412826842 -0.159312463 -0.127335663 -1.164570915
[51] 0.425077343 0.454675201 -0.403478381 -0.504487918 -0.053677979
[56] 0.739830381 -1.130567784 -0.069717679 -1.056333471 -0.544869060
[61] 2.275542119 0.559483937 1.430060430 -1.115133306 0.796833579
[66] 0.647732862 0.874890727 1.697912901 -0.141471235 -0.466059205
[71] 0.665296622 -0.239843407 0.284195631 0.473626512 0.903573678
[76] -0.892063358 0.569196401 -1.671882517 1.092067800 -0.925160786
[81] -0.158013492 1.390376882 -0.680171199 -1.420587175 -0.548727495
[86] -0.897782061 0.990272258 -0.888357406 0.129042914 0.225755491
[91] -0.799569813 0.263117022 0.360612964 0.148651062 1.412463379
[96] -0.907165816 -0.528513732 -1.307370272 -0.433195019 -0.714111720
> colMin(tmp)
[1] 0.665409686 1.088818726 1.243414626 0.803531133 -0.000698263
[6] -0.834704881 0.761433472 -1.578063908 0.127059218 0.200173507
[11] -0.364529983 -0.499905370 1.149904709 -0.329347352 1.103820277
[16] 0.347414136 -0.433689168 -0.342538472 0.194236102 0.753166806
[21] -1.490395540 -1.061591063 0.115948301 0.122238292 0.012600256
[26] 1.917545602 0.366278067 0.738799805 0.328381837 1.224323578
[31] 0.520245466 0.694093054 1.414438109 1.279585906 0.378594294
[36] 0.774978734 -1.082392630 0.008689405 1.071237232 0.063567511
[41] -1.895042857 -0.739346060 2.013216964 -1.314931194 -0.283739396
[46] -0.372752870 -0.412826842 -0.159312463 -0.127335663 -1.164570915
[51] 0.425077343 0.454675201 -0.403478381 -0.504487918 -0.053677979
[56] 0.739830381 -1.130567784 -0.069717679 -1.056333471 -0.544869060
[61] 2.275542119 0.559483937 1.430060430 -1.115133306 0.796833579
[66] 0.647732862 0.874890727 1.697912901 -0.141471235 -0.466059205
[71] 0.665296622 -0.239843407 0.284195631 0.473626512 0.903573678
[76] -0.892063358 0.569196401 -1.671882517 1.092067800 -0.925160786
[81] -0.158013492 1.390376882 -0.680171199 -1.420587175 -0.548727495
[86] -0.897782061 0.990272258 -0.888357406 0.129042914 0.225755491
[91] -0.799569813 0.263117022 0.360612964 0.148651062 1.412463379
[96] -0.907165816 -0.528513732 -1.307370272 -0.433195019 -0.714111720
> colMedians(tmp)
[1] 0.665409686 1.088818726 1.243414626 0.803531133 -0.000698263
[6] -0.834704881 0.761433472 -1.578063908 0.127059218 0.200173507
[11] -0.364529983 -0.499905370 1.149904709 -0.329347352 1.103820277
[16] 0.347414136 -0.433689168 -0.342538472 0.194236102 0.753166806
[21] -1.490395540 -1.061591063 0.115948301 0.122238292 0.012600256
[26] 1.917545602 0.366278067 0.738799805 0.328381837 1.224323578
[31] 0.520245466 0.694093054 1.414438109 1.279585906 0.378594294
[36] 0.774978734 -1.082392630 0.008689405 1.071237232 0.063567511
[41] -1.895042857 -0.739346060 2.013216964 -1.314931194 -0.283739396
[46] -0.372752870 -0.412826842 -0.159312463 -0.127335663 -1.164570915
[51] 0.425077343 0.454675201 -0.403478381 -0.504487918 -0.053677979
[56] 0.739830381 -1.130567784 -0.069717679 -1.056333471 -0.544869060
[61] 2.275542119 0.559483937 1.430060430 -1.115133306 0.796833579
[66] 0.647732862 0.874890727 1.697912901 -0.141471235 -0.466059205
[71] 0.665296622 -0.239843407 0.284195631 0.473626512 0.903573678
[76] -0.892063358 0.569196401 -1.671882517 1.092067800 -0.925160786
[81] -0.158013492 1.390376882 -0.680171199 -1.420587175 -0.548727495
[86] -0.897782061 0.990272258 -0.888357406 0.129042914 0.225755491
[91] -0.799569813 0.263117022 0.360612964 0.148651062 1.412463379
[96] -0.907165816 -0.528513732 -1.307370272 -0.433195019 -0.714111720
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.6654097 1.088819 1.243415 0.8035311 -0.000698263 -0.8347049 0.7614335
[2,] 0.6654097 1.088819 1.243415 0.8035311 -0.000698263 -0.8347049 0.7614335
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -1.578064 0.1270592 0.2001735 -0.36453 -0.4999054 1.149905 -0.3293474
[2,] -1.578064 0.1270592 0.2001735 -0.36453 -0.4999054 1.149905 -0.3293474
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 1.10382 0.3474141 -0.4336892 -0.3425385 0.1942361 0.7531668 -1.490396
[2,] 1.10382 0.3474141 -0.4336892 -0.3425385 0.1942361 0.7531668 -1.490396
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -1.061591 0.1159483 0.1222383 0.01260026 1.917546 0.3662781 0.7387998
[2,] -1.061591 0.1159483 0.1222383 0.01260026 1.917546 0.3662781 0.7387998
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.3283818 1.224324 0.5202455 0.6940931 1.414438 1.279586 0.3785943
[2,] 0.3283818 1.224324 0.5202455 0.6940931 1.414438 1.279586 0.3785943
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.7749787 -1.082393 0.008689405 1.071237 0.06356751 -1.895043 -0.7393461
[2,] 0.7749787 -1.082393 0.008689405 1.071237 0.06356751 -1.895043 -0.7393461
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 2.013217 -1.314931 -0.2837394 -0.3727529 -0.4128268 -0.1593125 -0.1273357
[2,] 2.013217 -1.314931 -0.2837394 -0.3727529 -0.4128268 -0.1593125 -0.1273357
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -1.164571 0.4250773 0.4546752 -0.4034784 -0.5044879 -0.05367798 0.7398304
[2,] -1.164571 0.4250773 0.4546752 -0.4034784 -0.5044879 -0.05367798 0.7398304
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -1.130568 -0.06971768 -1.056333 -0.5448691 2.275542 0.5594839 1.43006
[2,] -1.130568 -0.06971768 -1.056333 -0.5448691 2.275542 0.5594839 1.43006
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -1.115133 0.7968336 0.6477329 0.8748907 1.697913 -0.1414712 -0.4660592
[2,] -1.115133 0.7968336 0.6477329 0.8748907 1.697913 -0.1414712 -0.4660592
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 0.6652966 -0.2398434 0.2841956 0.4736265 0.9035737 -0.8920634 0.5691964
[2,] 0.6652966 -0.2398434 0.2841956 0.4736265 0.9035737 -0.8920634 0.5691964
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -1.671883 1.092068 -0.9251608 -0.1580135 1.390377 -0.6801712 -1.420587
[2,] -1.671883 1.092068 -0.9251608 -0.1580135 1.390377 -0.6801712 -1.420587
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -0.5487275 -0.8977821 0.9902723 -0.8883574 0.1290429 0.2257555 -0.7995698
[2,] -0.5487275 -0.8977821 0.9902723 -0.8883574 0.1290429 0.2257555 -0.7995698
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 0.263117 0.360613 0.1486511 1.412463 -0.9071658 -0.5285137 -1.30737
[2,] 0.263117 0.360613 0.1486511 1.412463 -0.9071658 -0.5285137 -1.30737
[,99] [,100]
[1,] -0.433195 -0.7141117
[2,] -0.433195 -0.7141117
>
>
> Max(tmp2)
[1] 2.541246
> Min(tmp2)
[1] -2.491714
> mean(tmp2)
[1] -0.07907371
> Sum(tmp2)
[1] -7.907371
> Var(tmp2)
[1] 0.9581165
>
> rowMeans(tmp2)
[1] 1.3276968071 0.7325931512 0.6332712729 0.2142934478 -0.6848051904
[6] -0.3891975042 0.8429504860 -0.4469166886 0.7673229104 -1.0678059504
[11] 1.3592934791 1.2451184165 -0.7196041667 -1.9668858280 -0.7192854522
[16] 0.2463333836 1.5792002790 0.0571641096 0.0870272316 0.0006907208
[21] -0.0907584164 -1.8231009827 -1.1458898536 -0.3956657370 0.7791095852
[26] 0.5882166416 -0.8163281458 -0.7408090528 -1.0810407751 -0.6118246135
[31] 0.5827582438 -1.0353742236 0.1190108200 1.8952774486 1.7577921359
[36] 0.3419766541 -0.8976439941 -0.8900584086 0.0806391717 -0.3315413066
[41] -0.7509422219 0.9578158102 0.1093710702 -1.0522315107 1.2297803140
[46] 0.7954943850 -0.6928404200 -0.5439315268 -0.6624256730 0.3356163838
[51] -1.2305563093 -0.0314580401 -0.1848564581 -0.6606444921 0.7564586002
[56] 0.7959005625 0.8830729520 -0.5182279712 0.7866802519 -1.0679240356
[61] 0.5700616774 -0.3750058480 -0.7727692421 -1.3223371468 -0.9017329241
[66] -1.3071271047 0.3965774700 0.8842827645 2.5412459558 1.5655747239
[71] 0.3883494151 -0.6921516822 -0.5161117399 -1.5007057132 -1.8869385786
[76] 0.6958368703 -2.4917138530 -1.1504002085 -1.7259915565 -0.4130994621
[81] 1.6929190200 -0.0689432612 -0.3457437683 -1.7407470649 0.7135455511
[86] 1.0910171873 -0.4651489294 -0.3325349319 -0.3920887390 0.1526577719
[91] -0.2975524272 0.6565460502 0.3364345532 0.8328060581 -0.4462705786
[96] -0.1453913199 -1.6198578387 1.5967374747 -0.0321620915 0.2832105873
> rowSums(tmp2)
[1] 1.3276968071 0.7325931512 0.6332712729 0.2142934478 -0.6848051904
[6] -0.3891975042 0.8429504860 -0.4469166886 0.7673229104 -1.0678059504
[11] 1.3592934791 1.2451184165 -0.7196041667 -1.9668858280 -0.7192854522
[16] 0.2463333836 1.5792002790 0.0571641096 0.0870272316 0.0006907208
[21] -0.0907584164 -1.8231009827 -1.1458898536 -0.3956657370 0.7791095852
[26] 0.5882166416 -0.8163281458 -0.7408090528 -1.0810407751 -0.6118246135
[31] 0.5827582438 -1.0353742236 0.1190108200 1.8952774486 1.7577921359
[36] 0.3419766541 -0.8976439941 -0.8900584086 0.0806391717 -0.3315413066
[41] -0.7509422219 0.9578158102 0.1093710702 -1.0522315107 1.2297803140
[46] 0.7954943850 -0.6928404200 -0.5439315268 -0.6624256730 0.3356163838
[51] -1.2305563093 -0.0314580401 -0.1848564581 -0.6606444921 0.7564586002
[56] 0.7959005625 0.8830729520 -0.5182279712 0.7866802519 -1.0679240356
[61] 0.5700616774 -0.3750058480 -0.7727692421 -1.3223371468 -0.9017329241
[66] -1.3071271047 0.3965774700 0.8842827645 2.5412459558 1.5655747239
[71] 0.3883494151 -0.6921516822 -0.5161117399 -1.5007057132 -1.8869385786
[76] 0.6958368703 -2.4917138530 -1.1504002085 -1.7259915565 -0.4130994621
[81] 1.6929190200 -0.0689432612 -0.3457437683 -1.7407470649 0.7135455511
[86] 1.0910171873 -0.4651489294 -0.3325349319 -0.3920887390 0.1526577719
[91] -0.2975524272 0.6565460502 0.3364345532 0.8328060581 -0.4462705786
[96] -0.1453913199 -1.6198578387 1.5967374747 -0.0321620915 0.2832105873
> rowVars(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowSd(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowMax(tmp2)
[1] 1.3276968071 0.7325931512 0.6332712729 0.2142934478 -0.6848051904
[6] -0.3891975042 0.8429504860 -0.4469166886 0.7673229104 -1.0678059504
[11] 1.3592934791 1.2451184165 -0.7196041667 -1.9668858280 -0.7192854522
[16] 0.2463333836 1.5792002790 0.0571641096 0.0870272316 0.0006907208
[21] -0.0907584164 -1.8231009827 -1.1458898536 -0.3956657370 0.7791095852
[26] 0.5882166416 -0.8163281458 -0.7408090528 -1.0810407751 -0.6118246135
[31] 0.5827582438 -1.0353742236 0.1190108200 1.8952774486 1.7577921359
[36] 0.3419766541 -0.8976439941 -0.8900584086 0.0806391717 -0.3315413066
[41] -0.7509422219 0.9578158102 0.1093710702 -1.0522315107 1.2297803140
[46] 0.7954943850 -0.6928404200 -0.5439315268 -0.6624256730 0.3356163838
[51] -1.2305563093 -0.0314580401 -0.1848564581 -0.6606444921 0.7564586002
[56] 0.7959005625 0.8830729520 -0.5182279712 0.7866802519 -1.0679240356
[61] 0.5700616774 -0.3750058480 -0.7727692421 -1.3223371468 -0.9017329241
[66] -1.3071271047 0.3965774700 0.8842827645 2.5412459558 1.5655747239
[71] 0.3883494151 -0.6921516822 -0.5161117399 -1.5007057132 -1.8869385786
[76] 0.6958368703 -2.4917138530 -1.1504002085 -1.7259915565 -0.4130994621
[81] 1.6929190200 -0.0689432612 -0.3457437683 -1.7407470649 0.7135455511
[86] 1.0910171873 -0.4651489294 -0.3325349319 -0.3920887390 0.1526577719
[91] -0.2975524272 0.6565460502 0.3364345532 0.8328060581 -0.4462705786
[96] -0.1453913199 -1.6198578387 1.5967374747 -0.0321620915 0.2832105873
> rowMin(tmp2)
[1] 1.3276968071 0.7325931512 0.6332712729 0.2142934478 -0.6848051904
[6] -0.3891975042 0.8429504860 -0.4469166886 0.7673229104 -1.0678059504
[11] 1.3592934791 1.2451184165 -0.7196041667 -1.9668858280 -0.7192854522
[16] 0.2463333836 1.5792002790 0.0571641096 0.0870272316 0.0006907208
[21] -0.0907584164 -1.8231009827 -1.1458898536 -0.3956657370 0.7791095852
[26] 0.5882166416 -0.8163281458 -0.7408090528 -1.0810407751 -0.6118246135
[31] 0.5827582438 -1.0353742236 0.1190108200 1.8952774486 1.7577921359
[36] 0.3419766541 -0.8976439941 -0.8900584086 0.0806391717 -0.3315413066
[41] -0.7509422219 0.9578158102 0.1093710702 -1.0522315107 1.2297803140
[46] 0.7954943850 -0.6928404200 -0.5439315268 -0.6624256730 0.3356163838
[51] -1.2305563093 -0.0314580401 -0.1848564581 -0.6606444921 0.7564586002
[56] 0.7959005625 0.8830729520 -0.5182279712 0.7866802519 -1.0679240356
[61] 0.5700616774 -0.3750058480 -0.7727692421 -1.3223371468 -0.9017329241
[66] -1.3071271047 0.3965774700 0.8842827645 2.5412459558 1.5655747239
[71] 0.3883494151 -0.6921516822 -0.5161117399 -1.5007057132 -1.8869385786
[76] 0.6958368703 -2.4917138530 -1.1504002085 -1.7259915565 -0.4130994621
[81] 1.6929190200 -0.0689432612 -0.3457437683 -1.7407470649 0.7135455511
[86] 1.0910171873 -0.4651489294 -0.3325349319 -0.3920887390 0.1526577719
[91] -0.2975524272 0.6565460502 0.3364345532 0.8328060581 -0.4462705786
[96] -0.1453913199 -1.6198578387 1.5967374747 -0.0321620915 0.2832105873
>
> colMeans(tmp2)
[1] -0.07907371
> colSums(tmp2)
[1] -7.907371
> colVars(tmp2)
[1] 0.9581165
> colSd(tmp2)
[1] 0.9788343
> colMax(tmp2)
[1] 2.541246
> colMin(tmp2)
[1] -2.491714
> colMedians(tmp2)
[1] -0.1180749
> colRanges(tmp2)
[,1]
[1,] -2.491714
[2,] 2.541246
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] 2.6168058 3.2379150 0.4147943 1.1364270 3.7710869 -0.5334487
[7] -2.7221456 -2.4483929 -5.2114147 -0.2669312
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.1412722
[2,] -0.4569497
[3,] 0.5084700
[4,] 0.9326424
[5,] 1.3751035
>
> rowApply(tmp,sum)
[1] -0.6720636 1.2896652 3.0608145 5.0259343 -5.9014011 2.7950686
[7] -4.0660875 -0.5788947 -1.0992430 0.1409031
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 8 2 9 3 7 10 7 8 8
[2,] 8 4 9 2 9 6 9 1 7 7
[3,] 10 9 8 7 4 8 2 4 1 1
[4,] 5 3 1 10 8 2 8 10 6 9
[5,] 9 6 10 5 10 9 4 2 9 5
[6,] 2 1 7 4 5 10 5 5 10 10
[7,] 7 7 5 1 6 3 1 9 5 4
[8,] 3 5 6 3 7 5 3 8 2 2
[9,] 4 2 4 6 1 1 7 6 4 3
[10,] 6 10 3 8 2 4 6 3 3 6
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] 3.62120294 1.23900818 1.30880072 3.29588971 -2.81183984 0.95975203
[7] 2.10500311 -1.39283587 1.71621478 -0.74652441 1.35923732 -5.21633165
[13] -2.06780302 0.37964232 -2.35235415 4.24987377 -0.02832606 -1.06076951
[19] 0.18721010 -1.44004067
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.6714634
[2,] 0.3959087
[3,] 1.1470919
[4,] 1.4665479
[5,] 2.2831178
>
> rowApply(tmp,sum)
[1] -0.4607034 8.6953951 -6.2494002 -4.3372231 5.6569414
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 14 19 20 2 18
[2,] 9 15 17 9 8
[3,] 19 16 16 4 6
[4,] 7 20 14 19 5
[5,] 12 3 6 7 7
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.3959087 -0.1415687 1.5119221 -0.4646957 0.09175462 1.2593571
[2,] 1.4665479 1.1129163 1.1442587 2.8287987 -0.58084008 1.1583084
[3,] 2.2831178 1.0206058 0.5991916 0.1629939 -0.96326623 -0.3947342
[4,] -1.6714634 -0.6093757 -1.4340291 1.3504467 -0.98754058 -0.4356912
[5,] 1.1470919 -0.1435695 -0.5125425 -0.5816539 -0.37194756 -0.6274881
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 1.7644765 -0.5621609 -0.02690491 0.32608725 0.495595304 0.6905872
[2,] 0.8020696 -0.3356033 0.27021218 -0.21189428 -0.009569136 -2.3487922
[3,] 0.1563253 -0.7139880 -0.47511272 -1.91939083 0.391358817 -2.0408633
[4,] -1.2044931 -0.2967900 1.33108212 1.14961491 -0.333213702 -2.0966780
[5,] 0.5866248 0.5157064 0.61693811 -0.09094147 0.815066039 0.5794146
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.4689154 -0.2170495 -0.1107813 0.4665692 -2.0833494 -0.9902881
[2,] 1.1060262 0.8527878 1.3445054 0.8365117 -0.4290929 -0.6858911
[3,] -2.3903067 -0.5514424 -2.0419012 0.1047393 1.9693039 -1.9033871
[4,] 0.8549334 -0.2187767 -0.9395796 1.1852570 1.2315961 1.5166141
[5,] -1.1695406 0.5141232 -0.6045974 1.6567966 -0.7167837 1.0021827
[,19] [,20]
[1,] -0.9430546 -1.4541928
[2,] 0.5891659 -0.2150307
[3,] 1.2077124 -0.7503561
[4,] -1.2887163 -1.4404200
[5,] 0.6221028 2.4199589
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.21-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-3.21-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 653 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.21-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-3.21-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 -0.595633 -2.822924 1.438448 -0.8959478 -0.7206594 -0.3246907 -0.3630965
col8 col9 col10 col11 col12 col13 col14
row1 0.1022423 0.4206607 1.803908 -1.140079 3.247855 1.032721 -0.3355332
col15 col16 col17 col18 col19 col20
row1 -1.409271 -0.03255137 0.2479349 -1.993956 -0.2872016 -0.04012773
> tmp[,"col10"]
col10
row1 1.8039078
row2 0.8260606
row3 -0.2838616
row4 -0.6206940
row5 0.2264885
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -0.595633 -2.8229237 1.4384483 -0.8959478 -0.7206594 -0.3246907 -0.3630965
row5 2.147858 -0.9761865 0.4458536 -0.5079454 1.0096907 0.9717771 1.1281630
col8 col9 col10 col11 col12 col13
row1 0.10224231 0.4206607 1.8039078 -1.1400793 3.2478551 1.0327214
row5 -0.06117962 -0.2697229 0.2264885 0.1390485 0.7881741 -0.5595042
col14 col15 col16 col17 col18 col19
row1 -0.3355332 -1.4092711 -0.03255137 0.2479349 -1.9939564 -0.2872016
row5 0.2744887 -0.8658335 0.32821989 0.1093865 -0.8600193 -1.3359910
col20
row1 -0.04012773
row5 0.61887782
> tmp[,c("col6","col20")]
col6 col20
row1 -0.3246907 -0.04012773
row2 0.1386150 0.26867300
row3 1.6869615 -2.20553600
row4 0.3913631 -0.15095717
row5 0.9717771 0.61887782
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -0.3246907 -0.04012773
row5 0.9717771 0.61887782
>
>
>
>
> 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 50.33877 49.94175 49.67209 49.05941 51.26873 103.3879 50.71041 50.44422
col9 col10 col11 col12 col13 col14 col15 col16
row1 48.01178 50.32394 51.8323 48.54287 50.76502 50.19174 49.98714 48.93452
col17 col18 col19 col20
row1 49.58218 49.78585 49.01325 105.7196
> tmp[,"col10"]
col10
row1 50.32394
row2 29.22985
row3 28.81794
row4 28.78185
row5 48.15722
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 50.33877 49.94175 49.67209 49.05941 51.26873 103.3879 50.71041 50.44422
row5 50.43724 47.86509 49.37746 49.20112 50.62047 106.2022 50.85002 50.87031
col9 col10 col11 col12 col13 col14 col15 col16
row1 48.01178 50.32394 51.83230 48.54287 50.76502 50.19174 49.98714 48.93452
row5 50.57859 48.15722 48.05968 48.86029 49.24761 49.94368 49.72546 50.07436
col17 col18 col19 col20
row1 49.58218 49.78585 49.01325 105.7196
row5 49.70568 49.17874 51.32522 104.2517
> tmp[,c("col6","col20")]
col6 col20
row1 103.38795 105.71955
row2 75.01311 75.54315
row3 74.39198 75.65087
row4 74.90873 74.66695
row5 106.20220 104.25174
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 103.3879 105.7196
row5 106.2022 104.2517
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 103.3879 105.7196
row5 106.2022 104.2517
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 1.2341438
[2,] -0.3496644
[3,] 0.9721473
[4,] -1.1392370
[5,] -0.4848378
> tmp[,c("col17","col7")]
col17 col7
[1,] 0.2359182 -1.71312941
[2,] -0.1042621 -0.44701697
[3,] -0.2174564 -0.71568922
[4,] -0.4279870 -0.08756406
[5,] -0.3476050 0.59564278
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.01748006 1.3184900
[2,] -0.83297959 -0.2345454
[3,] 0.31990903 -0.3191476
[4,] 0.20827343 -0.7725443
[5,] 0.44205309 -0.5674013
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.01748006
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.01748006
[2,] -0.83297959
>
>
>
> 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 1.5677466 -1.2934071 -0.921498 0.2648417 -0.3037530 0.9510502 0.196709
row1 -0.8988078 -0.6171002 -1.095219 0.6593104 -0.4647689 -0.3889032 -1.911519
[,8] [,9] [,10] [,11] [,12] [,13]
row3 0.9477200 -0.7162858 1.1203391 -0.7963099 0.5037897 1.4107134
row1 -0.1999368 0.3000859 -0.3589654 -0.3166806 1.7026016 -0.7476292
[,14] [,15] [,16] [,17] [,18] [,19]
row3 1.01680055 1.0074009 2.109989 0.9405640 -0.49449955 -0.4083688
row1 -0.09879325 -0.1451556 1.444783 -0.8491345 -0.07004393 0.4033860
[,20]
row3 -0.02693719
row1 -1.00684234
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 1.193889 0.5535718 0.6716336 -1.261257 0.6487617 -0.3349613 -0.0304952
[,8] [,9] [,10]
row2 0.7380569 0.3429206 -0.1128563
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 -1.065589 0.4181477 -1.152956 -0.5888411 0.4725883 0.5030949 0.9870725
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -1.402847 1.139423 1.07175 -1.992128 -0.8086816 0.8076477 0.8712549
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -0.01495701 -0.9644066 0.9585785 -0.08371851 -0.2512457 0.2070194
>
>
> 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: 0x581c45ddf5f0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests/BM262a854bbd5da5"
[2] "/home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests/BM262a853ff8f9b4"
[3] "/home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests/BM262a85575a7948"
[4] "/home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests/BM262a853487118e"
[5] "/home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests/BM262a8532f1dd4e"
[6] "/home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests/BM262a85147e821a"
[7] "/home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests/BM262a854dc9d28f"
[8] "/home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests/BM262a85414cc339"
[9] "/home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests/BM262a85320c1267"
[10] "/home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests/BM262a85c03cd2e"
[11] "/home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests/BM262a853b52ccd3"
[12] "/home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests/BM262a852a56f8a7"
[13] "/home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests/BM262a8521fb5d54"
[14] "/home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests/BM262a855c38ee05"
[15] "/home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests/BM262a85732d14f4"
>
>
> ### 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: 0x581c466ac360>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x581c466ac360>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.21-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x581c466ac360>
> rowMedians(tmp)
[1] 0.361043137 -0.287382758 -0.060189015 0.069037904 0.593791297
[6] -0.322513320 0.143257462 -0.171233672 -0.248617968 0.065584708
[11] -0.026910878 -0.380979005 -0.468569974 -0.429148086 0.125708355
[16] -0.152472387 0.544307533 -0.408026294 0.249452640 0.134381273
[21] 0.053360099 0.292772278 -0.232448997 -0.333319576 -0.478561494
[26] 0.218028173 0.531845037 0.045560522 0.615930460 -0.432569801
[31] 0.010280497 0.625883472 -0.286786348 0.385810093 0.141163308
[36] 0.496904915 0.008778561 -0.080762196 0.593250750 0.178765079
[41] -0.065174251 0.040691817 -0.621979323 -0.301395600 0.027057652
[46] -0.235933985 -0.482315488 0.004052884 0.158289215 0.158306736
[51] -0.203939637 -0.151374584 0.274437156 -0.175195964 0.374694302
[56] -0.178268755 0.277997463 -0.072359712 -0.367048970 0.656596997
[61] -0.188103337 -0.011363062 -0.166136521 0.097839368 0.152024779
[66] -0.255439930 -0.574534443 -0.427100105 -0.051944078 0.097032678
[71] -0.059956492 -0.303834704 -0.142836951 0.073197012 0.612136607
[76] -0.028008430 0.087896806 -0.012314702 0.271221197 -0.581579842
[81] -0.263685808 0.216257223 0.312253375 0.225440131 -0.221286553
[86] 0.471356023 -0.137725087 -0.137632697 0.207135428 0.459324720
[91] 0.020698259 0.295152592 0.280547992 0.358817433 0.011609056
[96] -0.231712267 0.041611142 -0.150164740 -0.230222833 0.704652236
[101] 0.465794804 -0.291286318 -0.134436034 -0.208274851 -0.345023152
[106] -0.072436991 -0.389376276 0.049678406 0.502755123 -0.347099628
[111] 0.094952358 0.035982981 -0.768414867 0.040686660 -0.221412779
[116] 0.430672234 -0.162206038 0.456440460 0.402769231 0.110891808
[121] 0.179587129 -0.151993439 -0.100268058 -0.469501824 0.194532707
[126] -0.343659067 -0.185457247 0.276199261 -0.084972027 0.290612830
[131] 0.394254979 -0.134651883 0.122404663 0.154039288 0.799518139
[136] -0.158723303 -0.225595169 0.266856793 0.254398050 -0.301366838
[141] -0.071612676 -0.523138152 0.184500347 -0.136222809 -0.257761959
[146] 0.309499095 -0.156217265 0.170153326 -0.230990566 -0.101412335
[151] 0.154453605 0.337492974 0.024480627 -0.228649760 -0.020929614
[156] 0.281501284 0.008514483 -0.493995176 0.025284514 0.533506979
[161] -0.313350798 0.360938331 0.384686570 0.212703225 0.814529901
[166] 0.012041477 -0.284849005 0.195459980 -0.360112930 -0.085956799
[171] 0.250206804 -0.084213463 -0.551031534 0.083610620 0.102081681
[176] -0.471727978 -0.284954676 0.112836267 0.262920539 -0.425807613
[181] 0.276016646 -0.798504216 -0.138822572 0.400653944 0.306086579
[186] -0.422093513 0.176167678 -0.533927389 0.014055382 0.263981591
[191] 0.467324585 -0.140612174 0.016724640 -0.338489981 0.451517395
[196] -0.095994592 0.402330299 0.162503427 -0.176159851 -0.186769999
[201] -0.613060931 0.105876688 -0.462786095 0.546452253 0.244005756
[206] -0.019815307 0.264124425 0.194749531 0.196372544 -0.142612525
[211] -0.424702518 0.013041515 0.274180366 -0.268598963 -0.873311567
[216] -0.114153569 -0.110381382 0.248486142 0.191159717 0.061514130
[221] -0.133657182 0.382284046 0.500847871 0.234414729 0.131042735
[226] 0.467914109 -0.007377844 -0.046808133 0.238003545 -0.003305964
>
> proc.time()
user system elapsed
1.309 1.509 2.806
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
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: 0x5bbbd12b1ad0>
> .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: 0x5bbbd12b1ad0>
> .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: 0x5bbbd12b1ad0>
> .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: 0x5bbbd12b1ad0>
> 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: 0x5bbbd12a3a30>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5bbbd12a3a30>
> .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: 0x5bbbd12a3a30>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5bbbd12a3a30>
> .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: 0x5bbbd12a3a30>
> 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: 0x5bbbd006f870>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5bbbd006f870>
> .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: 0x5bbbd006f870>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5bbbd006f870>
> .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: 0x5bbbd006f870>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x5bbbd006f870>
> .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: 0x5bbbd006f870>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x5bbbd006f870>
> .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: 0x5bbbd006f870>
> 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: 0x5bbbd04801a0>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x5bbbd04801a0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5bbbd04801a0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5bbbd04801a0>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile262d05457e4ca6" "BufferedMatrixFile262d055b2e4efb"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile262d05457e4ca6" "BufferedMatrixFile262d055b2e4efb"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x5bbbd262a870>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5bbbd262a870>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5bbbd262a870>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x5bbbd262a870>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x5bbbd262a870>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x5bbbd262a870>
> .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: 0x5bbbd0a7eca0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x5bbbd0a7eca0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x5bbbd0a7eca0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x5bbbd0a7eca0>
> 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: 0x5bbbd1231a20>
> .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: 0x5bbbd1231a20>
> rm(P)
>
> proc.time()
user system elapsed
0.244 0.051 0.283
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.234 0.053 0.276