| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:14:54 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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 | ||||
|
To the developers/maintainers of the BufferedMatrix package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 228/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.63.0 (landing page) Ben Bolstad
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: BufferedMatrix |
| Version: 1.63.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BufferedMatrix_1.63.0.tar.gz |
| StartedAt: 2023-02-06 19:43:16 -0000 (Mon, 06 Feb 2023) |
| EndedAt: 2023-02-06 19:43:48 -0000 (Mon, 06 Feb 2023) |
| EllapsedTime: 32.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BufferedMatrix_1.63.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.63.0’
* 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 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 R 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 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
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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘BufferedMatrix.Rnw’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘BufferedMatrix’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -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){
| ^~~~~~~~~~~~~~~~~~~
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 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c init_package.c -o init_package.o
gcc -shared -L/home/biocbuild/bbs-3.17-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-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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
0.346 0.026 0.357
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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-3.17-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 456993 24.5 979984 52.4 651420 34.8
Vcells 842364 6.5 8388608 64.0 2047783 15.7
>
>
>
>
> ##
> ## 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] "Mon Feb 6 19:43:35 2023"
> 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] "Mon Feb 6 19:43:35 2023"
>
>
> 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: 0xaaaae69778e0>
>
>
>
> 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] "Mon Feb 6 19:43:36 2023"
> 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] "Mon Feb 6 19:43:36 2023"
>
> ColMode(tmp2)
<pointer: 0xaaaae69778e0>
>
>
>
> ### 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,] 99.8340965 0.02021106 0.2670532 -1.5349296
[2,] -1.3360961 1.29036535 1.2409206 0.4875652
[3,] -0.3816884 1.42004983 -0.9518254 -1.4060628
[4,] 0.5077188 -2.81514285 -2.3611427 0.8043706
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.17-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,] 99.8340965 0.02021106 0.2670532 1.5349296
[2,] 1.3360961 1.29036535 1.2409206 0.4875652
[3,] 0.3816884 1.42004983 0.9518254 1.4060628
[4,] 0.5077188 2.81514285 2.3611427 0.8043706
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 2 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 9.9917014 0.1421656 0.5167719 1.2389227
[2,] 1.1558962 1.1359425 1.1139662 0.6982587
[3,] 0.6178093 1.1916584 0.9756154 1.1857752
[4,] 0.7125439 1.6778387 1.5366010 0.8968671
>
> 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-3.17-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,] 224.75111 26.44187 30.43477 38.92416
[2,] 37.89506 37.64979 37.38058 32.47015
[3,] 31.55978 38.33663 35.70798 38.26381
[4,] 32.63316 44.59353 42.72715 34.77304
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0xaaaae60f6470>
> exp(tmp5)
<pointer: 0xaaaae60f6470>
> log(tmp5,2)
<pointer: 0xaaaae60f6470>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 467.79
> Min(tmp5)
[1] 53.62108
> mean(tmp5)
[1] 73.39161
> Sum(tmp5)
[1] 14678.32
> Var(tmp5)
[1] 859.5135
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 92.21983 68.49317 71.85821 78.62963 70.02766 69.29431 71.39794 71.42415
[9] 70.78867 69.78248
> rowSums(tmp5)
[1] 1844.397 1369.863 1437.164 1572.593 1400.553 1385.886 1427.959 1428.483
[9] 1415.773 1395.650
> rowVars(tmp5)
[1] 7903.09605 105.73683 65.22636 72.52306 65.07901 84.25372
[7] 61.54198 67.29367 33.48343 55.58048
> rowSd(tmp5)
[1] 88.899359 10.282842 8.076284 8.516047 8.067156 9.178983 7.844870
[8] 8.203272 5.786487 7.455232
> rowMax(tmp5)
[1] 467.78999 83.65336 81.32947 92.81559 86.17121 93.33132 88.22190
[8] 82.12544 80.54518 84.72113
> rowMin(tmp5)
[1] 55.03528 53.62108 53.72545 63.21452 54.58390 53.89311 56.36048 55.94562
[9] 58.20816 58.70263
>
> colMeans(tmp5)
[1] 110.08318 72.67405 71.23350 73.68817 75.08311 69.01153 73.40787
[8] 66.69818 71.08296 71.57443 73.76759 71.32612 71.67541 66.26323
[15] 64.81622 76.64561 73.37081 73.82902 68.07978 73.52133
> colSums(tmp5)
[1] 1100.8318 726.7405 712.3350 736.8817 750.8311 690.1153 734.0787
[8] 666.9818 710.8296 715.7443 737.6759 713.2612 716.7541 662.6323
[15] 648.1622 766.4561 733.7081 738.2902 680.7978 735.2133
> colVars(tmp5)
[1] 15810.76870 126.68620 81.98593 33.44273 78.76942 80.91683
[7] 84.37114 75.44366 79.86922 27.76626 101.10572 96.31585
[13] 77.20396 21.48541 47.18433 59.28016 127.00932 66.67762
[19] 94.39398 58.86756
> colSd(tmp5)
[1] 125.740879 11.255496 9.054608 5.782969 8.875214 8.995378
[7] 9.185376 8.685831 8.936958 5.269370 10.055134 9.814064
[13] 8.786578 4.635236 6.869085 7.699361 11.269841 8.165636
[19] 9.715656 7.672520
> colMax(tmp5)
[1] 467.78999 92.81559 88.93097 81.29221 86.14849 79.43307 93.33132
[8] 82.12544 82.48015 79.39467 88.22190 88.49674 84.72113 73.56661
[15] 76.32619 87.40440 90.92851 83.65336 81.32947 87.19155
> colMin(tmp5)
[1] 65.68755 55.03528 58.23513 64.83396 58.37490 55.85254 58.70263 53.89311
[9] 54.24847 60.57780 60.64110 57.18194 53.72545 57.85688 55.60856 61.90247
[17] 53.62108 57.34916 54.58390 63.94024
>
>
> ### 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] 92.21983 68.49317 NA 78.62963 70.02766 69.29431 71.39794 71.42415
[9] 70.78867 69.78248
> rowSums(tmp5)
[1] 1844.397 1369.863 NA 1572.593 1400.553 1385.886 1427.959 1428.483
[9] 1415.773 1395.650
> rowVars(tmp5)
[1] 7903.09605 105.73683 67.97058 72.52306 65.07901 84.25372
[7] 61.54198 67.29367 33.48343 55.58048
> rowSd(tmp5)
[1] 88.899359 10.282842 8.244427 8.516047 8.067156 9.178983 7.844870
[8] 8.203272 5.786487 7.455232
> rowMax(tmp5)
[1] 467.78999 83.65336 NA 92.81559 86.17121 93.33132 88.22190
[8] 82.12544 80.54518 84.72113
> rowMin(tmp5)
[1] 55.03528 53.62108 NA 63.21452 54.58390 53.89311 56.36048 55.94562
[9] 58.20816 58.70263
>
> colMeans(tmp5)
[1] 110.08318 72.67405 71.23350 73.68817 75.08311 69.01153 73.40787
[8] 66.69818 71.08296 71.57443 73.76759 NA 71.67541 66.26323
[15] 64.81622 76.64561 73.37081 73.82902 68.07978 73.52133
> colSums(tmp5)
[1] 1100.8318 726.7405 712.3350 736.8817 750.8311 690.1153 734.0787
[8] 666.9818 710.8296 715.7443 737.6759 NA 716.7541 662.6323
[15] 648.1622 766.4561 733.7081 738.2902 680.7978 735.2133
> colVars(tmp5)
[1] 15810.76870 126.68620 81.98593 33.44273 78.76942 80.91683
[7] 84.37114 75.44366 79.86922 27.76626 101.10572 NA
[13] 77.20396 21.48541 47.18433 59.28016 127.00932 66.67762
[19] 94.39398 58.86756
> colSd(tmp5)
[1] 125.740879 11.255496 9.054608 5.782969 8.875214 8.995378
[7] 9.185376 8.685831 8.936958 5.269370 10.055134 NA
[13] 8.786578 4.635236 6.869085 7.699361 11.269841 8.165636
[19] 9.715656 7.672520
> colMax(tmp5)
[1] 467.78999 92.81559 88.93097 81.29221 86.14849 79.43307 93.33132
[8] 82.12544 82.48015 79.39467 88.22190 NA 84.72113 73.56661
[15] 76.32619 87.40440 90.92851 83.65336 81.32947 87.19155
> colMin(tmp5)
[1] 65.68755 55.03528 58.23513 64.83396 58.37490 55.85254 58.70263 53.89311
[9] 54.24847 60.57780 60.64110 NA 53.72545 57.85688 55.60856 61.90247
[17] 53.62108 57.34916 54.58390 63.94024
>
> Max(tmp5,na.rm=TRUE)
[1] 467.79
> Min(tmp5,na.rm=TRUE)
[1] 53.62108
> mean(tmp5,na.rm=TRUE)
[1] 73.4188
> Sum(tmp5,na.rm=TRUE)
[1] 14610.34
> Var(tmp5,na.rm=TRUE)
[1] 863.7058
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.21983 68.49317 72.06231 78.62963 70.02766 69.29431 71.39794 71.42415
[9] 70.78867 69.78248
> rowSums(tmp5,na.rm=TRUE)
[1] 1844.397 1369.863 1369.184 1572.593 1400.553 1385.886 1427.959 1428.483
[9] 1415.773 1395.650
> rowVars(tmp5,na.rm=TRUE)
[1] 7903.09605 105.73683 67.97058 72.52306 65.07901 84.25372
[7] 61.54198 67.29367 33.48343 55.58048
> rowSd(tmp5,na.rm=TRUE)
[1] 88.899359 10.282842 8.244427 8.516047 8.067156 9.178983 7.844870
[8] 8.203272 5.786487 7.455232
> rowMax(tmp5,na.rm=TRUE)
[1] 467.78999 83.65336 81.32947 92.81559 86.17121 93.33132 88.22190
[8] 82.12544 80.54518 84.72113
> rowMin(tmp5,na.rm=TRUE)
[1] 55.03528 53.62108 53.72545 63.21452 54.58390 53.89311 56.36048 55.94562
[9] 58.20816 58.70263
>
> colMeans(tmp5,na.rm=TRUE)
[1] 110.08318 72.67405 71.23350 73.68817 75.08311 69.01153 73.40787
[8] 66.69818 71.08296 71.57443 73.76759 71.69789 71.67541 66.26323
[15] 64.81622 76.64561 73.37081 73.82902 68.07978 73.52133
> colSums(tmp5,na.rm=TRUE)
[1] 1100.8318 726.7405 712.3350 736.8817 750.8311 690.1153 734.0787
[8] 666.9818 710.8296 715.7443 737.6759 645.2810 716.7541 662.6323
[15] 648.1622 766.4561 733.7081 738.2902 680.7978 735.2133
> colVars(tmp5,na.rm=TRUE)
[1] 15810.76870 126.68620 81.98593 33.44273 78.76942 80.91683
[7] 84.37114 75.44366 79.86922 27.76626 101.10572 106.80045
[13] 77.20396 21.48541 47.18433 59.28016 127.00932 66.67762
[19] 94.39398 58.86756
> colSd(tmp5,na.rm=TRUE)
[1] 125.740879 11.255496 9.054608 5.782969 8.875214 8.995378
[7] 9.185376 8.685831 8.936958 5.269370 10.055134 10.334430
[13] 8.786578 4.635236 6.869085 7.699361 11.269841 8.165636
[19] 9.715656 7.672520
> colMax(tmp5,na.rm=TRUE)
[1] 467.78999 92.81559 88.93097 81.29221 86.14849 79.43307 93.33132
[8] 82.12544 82.48015 79.39467 88.22190 88.49674 84.72113 73.56661
[15] 76.32619 87.40440 90.92851 83.65336 81.32947 87.19155
> colMin(tmp5,na.rm=TRUE)
[1] 65.68755 55.03528 58.23513 64.83396 58.37490 55.85254 58.70263 53.89311
[9] 54.24847 60.57780 60.64110 57.18194 53.72545 57.85688 55.60856 61.90247
[17] 53.62108 57.34916 54.58390 63.94024
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 92.21983 68.49317 NaN 78.62963 70.02766 69.29431 71.39794 71.42415
[9] 70.78867 69.78248
> rowSums(tmp5,na.rm=TRUE)
[1] 1844.397 1369.863 0.000 1572.593 1400.553 1385.886 1427.959 1428.483
[9] 1415.773 1395.650
> rowVars(tmp5,na.rm=TRUE)
[1] 7903.09605 105.73683 NA 72.52306 65.07901 84.25372
[7] 61.54198 67.29367 33.48343 55.58048
> rowSd(tmp5,na.rm=TRUE)
[1] 88.899359 10.282842 NA 8.516047 8.067156 9.178983 7.844870
[8] 8.203272 5.786487 7.455232
> rowMax(tmp5,na.rm=TRUE)
[1] 467.78999 83.65336 NA 92.81559 86.17121 93.33132 88.22190
[8] 82.12544 80.54518 84.72113
> rowMin(tmp5,na.rm=TRUE)
[1] 55.03528 53.62108 NA 63.21452 54.58390 53.89311 56.36048 55.94562
[9] 58.20816 58.70263
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 115.01603 71.88309 70.89039 73.02673 74.82975 68.23351 73.00522
[8] 67.48739 72.37875 71.19637 73.21553 NaN 73.66985 66.28826
[15] 64.36390 76.18220 72.73424 74.33527 66.60759 74.19768
> colSums(tmp5,na.rm=TRUE)
[1] 1035.1443 646.9478 638.0135 657.2406 673.4678 614.1016 657.0470
[8] 607.3865 651.4087 640.7673 658.9398 0.0000 663.0286 596.5943
[15] 579.2751 685.6398 654.6082 669.0175 599.4683 667.7791
> colVars(tmp5,na.rm=TRUE)
[1] 17513.36866 135.48379 90.90979 32.70118 87.89348 84.22174
[7] 93.09361 77.86704 70.96347 29.62910 110.31529 NA
[13] 42.10430 24.16404 50.78071 64.27427 138.32672 72.12905
[19] 81.81070 61.07971
> colSd(tmp5,na.rm=TRUE)
[1] 132.338085 11.639751 9.534662 5.718495 9.375152 9.177240
[7] 9.648503 8.824230 8.423982 5.443262 10.503109 NA
[13] 6.488783 4.915693 7.126058 8.017123 11.761238 8.492883
[19] 9.044927 7.815351
> colMax(tmp5,na.rm=TRUE)
[1] 467.78999 92.81559 88.93097 81.29221 86.14849 79.43307 93.33132
[8] 82.12544 82.48015 79.39467 88.22190 -Inf 84.72113 73.56661
[15] 76.32619 87.40440 90.92851 83.65336 80.05394 87.19155
> colMin(tmp5,na.rm=TRUE)
[1] 65.98660 55.03528 58.23513 64.83396 58.37490 55.85254 58.70263 53.89311
[9] 54.24847 60.57780 60.64110 Inf 64.67902 57.85688 55.60856 61.90247
[17] 53.62108 57.34916 54.58390 63.94024
>
>
>
>
> 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] 133.5209 289.7186 184.5217 213.4885 223.2248 126.5134 422.5606 105.2870
[9] 227.5293 281.5015
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 133.5209 289.7186 184.5217 213.4885 223.2248 126.5134 422.5606 105.2870
[9] 227.5293 281.5015
>
>
>
> 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 5.684342e-14 5.684342e-14 5.684342e-14 -1.136868e-13
[6] -1.421085e-13 0.000000e+00 -1.136868e-13 2.842171e-13 -1.989520e-13
[11] 1.421085e-13 -1.421085e-14 2.842171e-14 8.526513e-14 1.136868e-13
[16] -5.684342e-14 -8.526513e-14 0.000000e+00 -5.684342e-14 -1.136868e-13
>
>
>
>
>
>
>
>
>
>
> ## 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 2
5 10
7 8
3 14
9 4
10 3
7 9
2 14
9 17
3 9
9 16
1 18
8 6
9 4
3 20
5 18
3 4
9 4
1 20
9 19
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] 2.457633
> Min(tmp)
[1] -1.982932
> mean(tmp)
[1] 0.05674519
> Sum(tmp)
[1] 5.674519
> Var(tmp)
[1] 0.9243427
>
> rowMeans(tmp)
[1] 0.05674519
> rowSums(tmp)
[1] 5.674519
> rowVars(tmp)
[1] 0.9243427
> rowSd(tmp)
[1] 0.9614274
> rowMax(tmp)
[1] 2.457633
> rowMin(tmp)
[1] -1.982932
>
> colMeans(tmp)
[1] -1.58707985 0.43134122 -0.26840270 -0.04770171 -0.90292160 0.93456646
[7] 0.26036317 0.94170377 -1.40070639 -0.30117065 0.21959168 0.71603217
[13] -0.34508677 0.84080296 1.09025413 -1.98293209 -0.54793678 -0.42270688
[19] 0.31116683 0.53246145 0.01253387 -0.35584959 -0.36328947 1.07750681
[25] -0.86991657 2.25916474 -1.84671705 -0.27344931 0.56798301 0.22277900
[31] 0.72985506 -1.06709275 0.77397673 -0.15607902 -1.39488458 1.11153453
[37] -1.71322809 1.29944543 1.77450145 -1.75446758 0.62920907 0.18136640
[43] -1.57654877 -0.34515045 -1.04769173 0.34794179 0.89012489 -1.12009290
[49] -0.78467062 -0.33297403 1.19539772 1.67093463 -0.14047816 1.39343113
[55] 1.56839476 0.43069655 0.64445114 -0.63557458 0.95151354 -1.53302237
[61] 0.40336828 -1.22719877 -1.09476680 0.26744251 0.08015068 1.66228213
[67] 0.45844335 -0.45252242 -1.03407856 -0.92384321 0.11845848 0.68316644
[73] -0.28725956 0.98429098 1.10477371 0.35608857 -0.14525290 -0.57534755
[79] 0.92299187 2.45763257 0.22202322 -0.38413020 -0.47101066 -0.57301822
[85] -0.98394513 0.43490675 -0.77991284 1.20103462 0.50178684 1.01267567
[91] 0.29245217 0.18000028 1.36360530 -1.61704752 0.30418247 0.59885471
[97] 0.17903631 -0.12282361 0.55589607 -0.89206999
> colSums(tmp)
[1] -1.58707985 0.43134122 -0.26840270 -0.04770171 -0.90292160 0.93456646
[7] 0.26036317 0.94170377 -1.40070639 -0.30117065 0.21959168 0.71603217
[13] -0.34508677 0.84080296 1.09025413 -1.98293209 -0.54793678 -0.42270688
[19] 0.31116683 0.53246145 0.01253387 -0.35584959 -0.36328947 1.07750681
[25] -0.86991657 2.25916474 -1.84671705 -0.27344931 0.56798301 0.22277900
[31] 0.72985506 -1.06709275 0.77397673 -0.15607902 -1.39488458 1.11153453
[37] -1.71322809 1.29944543 1.77450145 -1.75446758 0.62920907 0.18136640
[43] -1.57654877 -0.34515045 -1.04769173 0.34794179 0.89012489 -1.12009290
[49] -0.78467062 -0.33297403 1.19539772 1.67093463 -0.14047816 1.39343113
[55] 1.56839476 0.43069655 0.64445114 -0.63557458 0.95151354 -1.53302237
[61] 0.40336828 -1.22719877 -1.09476680 0.26744251 0.08015068 1.66228213
[67] 0.45844335 -0.45252242 -1.03407856 -0.92384321 0.11845848 0.68316644
[73] -0.28725956 0.98429098 1.10477371 0.35608857 -0.14525290 -0.57534755
[79] 0.92299187 2.45763257 0.22202322 -0.38413020 -0.47101066 -0.57301822
[85] -0.98394513 0.43490675 -0.77991284 1.20103462 0.50178684 1.01267567
[91] 0.29245217 0.18000028 1.36360530 -1.61704752 0.30418247 0.59885471
[97] 0.17903631 -0.12282361 0.55589607 -0.89206999
> 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] -1.58707985 0.43134122 -0.26840270 -0.04770171 -0.90292160 0.93456646
[7] 0.26036317 0.94170377 -1.40070639 -0.30117065 0.21959168 0.71603217
[13] -0.34508677 0.84080296 1.09025413 -1.98293209 -0.54793678 -0.42270688
[19] 0.31116683 0.53246145 0.01253387 -0.35584959 -0.36328947 1.07750681
[25] -0.86991657 2.25916474 -1.84671705 -0.27344931 0.56798301 0.22277900
[31] 0.72985506 -1.06709275 0.77397673 -0.15607902 -1.39488458 1.11153453
[37] -1.71322809 1.29944543 1.77450145 -1.75446758 0.62920907 0.18136640
[43] -1.57654877 -0.34515045 -1.04769173 0.34794179 0.89012489 -1.12009290
[49] -0.78467062 -0.33297403 1.19539772 1.67093463 -0.14047816 1.39343113
[55] 1.56839476 0.43069655 0.64445114 -0.63557458 0.95151354 -1.53302237
[61] 0.40336828 -1.22719877 -1.09476680 0.26744251 0.08015068 1.66228213
[67] 0.45844335 -0.45252242 -1.03407856 -0.92384321 0.11845848 0.68316644
[73] -0.28725956 0.98429098 1.10477371 0.35608857 -0.14525290 -0.57534755
[79] 0.92299187 2.45763257 0.22202322 -0.38413020 -0.47101066 -0.57301822
[85] -0.98394513 0.43490675 -0.77991284 1.20103462 0.50178684 1.01267567
[91] 0.29245217 0.18000028 1.36360530 -1.61704752 0.30418247 0.59885471
[97] 0.17903631 -0.12282361 0.55589607 -0.89206999
> colMin(tmp)
[1] -1.58707985 0.43134122 -0.26840270 -0.04770171 -0.90292160 0.93456646
[7] 0.26036317 0.94170377 -1.40070639 -0.30117065 0.21959168 0.71603217
[13] -0.34508677 0.84080296 1.09025413 -1.98293209 -0.54793678 -0.42270688
[19] 0.31116683 0.53246145 0.01253387 -0.35584959 -0.36328947 1.07750681
[25] -0.86991657 2.25916474 -1.84671705 -0.27344931 0.56798301 0.22277900
[31] 0.72985506 -1.06709275 0.77397673 -0.15607902 -1.39488458 1.11153453
[37] -1.71322809 1.29944543 1.77450145 -1.75446758 0.62920907 0.18136640
[43] -1.57654877 -0.34515045 -1.04769173 0.34794179 0.89012489 -1.12009290
[49] -0.78467062 -0.33297403 1.19539772 1.67093463 -0.14047816 1.39343113
[55] 1.56839476 0.43069655 0.64445114 -0.63557458 0.95151354 -1.53302237
[61] 0.40336828 -1.22719877 -1.09476680 0.26744251 0.08015068 1.66228213
[67] 0.45844335 -0.45252242 -1.03407856 -0.92384321 0.11845848 0.68316644
[73] -0.28725956 0.98429098 1.10477371 0.35608857 -0.14525290 -0.57534755
[79] 0.92299187 2.45763257 0.22202322 -0.38413020 -0.47101066 -0.57301822
[85] -0.98394513 0.43490675 -0.77991284 1.20103462 0.50178684 1.01267567
[91] 0.29245217 0.18000028 1.36360530 -1.61704752 0.30418247 0.59885471
[97] 0.17903631 -0.12282361 0.55589607 -0.89206999
> colMedians(tmp)
[1] -1.58707985 0.43134122 -0.26840270 -0.04770171 -0.90292160 0.93456646
[7] 0.26036317 0.94170377 -1.40070639 -0.30117065 0.21959168 0.71603217
[13] -0.34508677 0.84080296 1.09025413 -1.98293209 -0.54793678 -0.42270688
[19] 0.31116683 0.53246145 0.01253387 -0.35584959 -0.36328947 1.07750681
[25] -0.86991657 2.25916474 -1.84671705 -0.27344931 0.56798301 0.22277900
[31] 0.72985506 -1.06709275 0.77397673 -0.15607902 -1.39488458 1.11153453
[37] -1.71322809 1.29944543 1.77450145 -1.75446758 0.62920907 0.18136640
[43] -1.57654877 -0.34515045 -1.04769173 0.34794179 0.89012489 -1.12009290
[49] -0.78467062 -0.33297403 1.19539772 1.67093463 -0.14047816 1.39343113
[55] 1.56839476 0.43069655 0.64445114 -0.63557458 0.95151354 -1.53302237
[61] 0.40336828 -1.22719877 -1.09476680 0.26744251 0.08015068 1.66228213
[67] 0.45844335 -0.45252242 -1.03407856 -0.92384321 0.11845848 0.68316644
[73] -0.28725956 0.98429098 1.10477371 0.35608857 -0.14525290 -0.57534755
[79] 0.92299187 2.45763257 0.22202322 -0.38413020 -0.47101066 -0.57301822
[85] -0.98394513 0.43490675 -0.77991284 1.20103462 0.50178684 1.01267567
[91] 0.29245217 0.18000028 1.36360530 -1.61704752 0.30418247 0.59885471
[97] 0.17903631 -0.12282361 0.55589607 -0.89206999
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] -1.58708 0.4313412 -0.2684027 -0.04770171 -0.9029216 0.9345665 0.2603632
[2,] -1.58708 0.4313412 -0.2684027 -0.04770171 -0.9029216 0.9345665 0.2603632
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 0.9417038 -1.400706 -0.3011706 0.2195917 0.7160322 -0.3450868 0.840803
[2,] 0.9417038 -1.400706 -0.3011706 0.2195917 0.7160322 -0.3450868 0.840803
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] 1.090254 -1.982932 -0.5479368 -0.4227069 0.3111668 0.5324614 0.01253387
[2,] 1.090254 -1.982932 -0.5479368 -0.4227069 0.3111668 0.5324614 0.01253387
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.3558496 -0.3632895 1.077507 -0.8699166 2.259165 -1.846717 -0.2734493
[2,] -0.3558496 -0.3632895 1.077507 -0.8699166 2.259165 -1.846717 -0.2734493
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 0.567983 0.222779 0.7298551 -1.067093 0.7739767 -0.156079 -1.394885
[2,] 0.567983 0.222779 0.7298551 -1.067093 0.7739767 -0.156079 -1.394885
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 1.111535 -1.713228 1.299445 1.774501 -1.754468 0.6292091 0.1813664
[2,] 1.111535 -1.713228 1.299445 1.774501 -1.754468 0.6292091 0.1813664
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -1.576549 -0.3451505 -1.047692 0.3479418 0.8901249 -1.120093 -0.7846706
[2,] -1.576549 -0.3451505 -1.047692 0.3479418 0.8901249 -1.120093 -0.7846706
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -0.332974 1.195398 1.670935 -0.1404782 1.393431 1.568395 0.4306966
[2,] -0.332974 1.195398 1.670935 -0.1404782 1.393431 1.568395 0.4306966
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.6444511 -0.6355746 0.9515135 -1.533022 0.4033683 -1.227199 -1.094767
[2,] 0.6444511 -0.6355746 0.9515135 -1.533022 0.4033683 -1.227199 -1.094767
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.2674425 0.08015068 1.662282 0.4584433 -0.4525224 -1.034079 -0.9238432
[2,] 0.2674425 0.08015068 1.662282 0.4584433 -0.4525224 -1.034079 -0.9238432
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 0.1184585 0.6831664 -0.2872596 0.984291 1.104774 0.3560886 -0.1452529
[2,] 0.1184585 0.6831664 -0.2872596 0.984291 1.104774 0.3560886 -0.1452529
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] -0.5753476 0.9229919 2.457633 0.2220232 -0.3841302 -0.4710107 -0.5730182
[2,] -0.5753476 0.9229919 2.457633 0.2220232 -0.3841302 -0.4710107 -0.5730182
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -0.9839451 0.4349068 -0.7799128 1.201035 0.5017868 1.012676 0.2924522
[2,] -0.9839451 0.4349068 -0.7799128 1.201035 0.5017868 1.012676 0.2924522
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 0.1800003 1.363605 -1.617048 0.3041825 0.5988547 0.1790363 -0.1228236
[2,] 0.1800003 1.363605 -1.617048 0.3041825 0.5988547 0.1790363 -0.1228236
[,99] [,100]
[1,] 0.5558961 -0.89207
[2,] 0.5558961 -0.89207
>
>
> Max(tmp2)
[1] 3.215825
> Min(tmp2)
[1] -2.052792
> mean(tmp2)
[1] 0.1039996
> Sum(tmp2)
[1] 10.39996
> Var(tmp2)
[1] 0.8770364
>
> rowMeans(tmp2)
[1] 0.67432711 -0.34875215 -0.64636814 -0.63846120 0.11030333 -0.04132767
[7] -0.04089171 -2.05279164 -0.37694750 0.85364008 -0.06204956 1.57383868
[13] -0.59076570 3.21582454 1.46389154 2.18139857 -0.81073297 0.91366085
[19] 0.34025996 -0.29069211 0.16053132 1.15328157 -0.18413379 1.49097207
[25] 0.85019058 0.49975473 0.02254259 -1.14038571 -0.11366888 -0.21299747
[31] -0.64761130 0.76845520 2.18328708 -1.15259755 0.76494864 -0.43264619
[37] -1.04034121 -0.81423582 0.55262987 0.16582805 -0.73351240 -0.59687769
[43] 0.09386606 0.07445605 0.14287530 0.47315553 -0.56464216 -0.72948610
[49] -0.67198456 0.51012053 0.71665700 0.18357668 0.24903393 -0.92575091
[55] 0.44106182 -0.71553985 -2.04850844 0.04946201 -0.46343839 0.48855622
[61] -0.67916195 1.65681914 -0.51641031 0.94688443 0.74149074 0.60670684
[67] -0.92248354 -1.50940345 0.11396558 -0.27022434 -0.11619359 -0.23814117
[73] 0.14480153 0.12544927 0.97402258 0.82005646 1.01329028 0.51574488
[79] -0.62734008 0.12352506 0.60822962 -0.25296197 1.76974309 -1.34371710
[85] 0.90558724 1.11478870 -0.54830971 -1.05716697 -1.93140674 0.66382524
[91] -0.63875714 1.52315037 -0.65309526 1.62243612 -0.15394501 -0.08823283
[97] 0.22034360 -0.30656968 1.81138325 -0.04301440
> rowSums(tmp2)
[1] 0.67432711 -0.34875215 -0.64636814 -0.63846120 0.11030333 -0.04132767
[7] -0.04089171 -2.05279164 -0.37694750 0.85364008 -0.06204956 1.57383868
[13] -0.59076570 3.21582454 1.46389154 2.18139857 -0.81073297 0.91366085
[19] 0.34025996 -0.29069211 0.16053132 1.15328157 -0.18413379 1.49097207
[25] 0.85019058 0.49975473 0.02254259 -1.14038571 -0.11366888 -0.21299747
[31] -0.64761130 0.76845520 2.18328708 -1.15259755 0.76494864 -0.43264619
[37] -1.04034121 -0.81423582 0.55262987 0.16582805 -0.73351240 -0.59687769
[43] 0.09386606 0.07445605 0.14287530 0.47315553 -0.56464216 -0.72948610
[49] -0.67198456 0.51012053 0.71665700 0.18357668 0.24903393 -0.92575091
[55] 0.44106182 -0.71553985 -2.04850844 0.04946201 -0.46343839 0.48855622
[61] -0.67916195 1.65681914 -0.51641031 0.94688443 0.74149074 0.60670684
[67] -0.92248354 -1.50940345 0.11396558 -0.27022434 -0.11619359 -0.23814117
[73] 0.14480153 0.12544927 0.97402258 0.82005646 1.01329028 0.51574488
[79] -0.62734008 0.12352506 0.60822962 -0.25296197 1.76974309 -1.34371710
[85] 0.90558724 1.11478870 -0.54830971 -1.05716697 -1.93140674 0.66382524
[91] -0.63875714 1.52315037 -0.65309526 1.62243612 -0.15394501 -0.08823283
[97] 0.22034360 -0.30656968 1.81138325 -0.04301440
> 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] 0.67432711 -0.34875215 -0.64636814 -0.63846120 0.11030333 -0.04132767
[7] -0.04089171 -2.05279164 -0.37694750 0.85364008 -0.06204956 1.57383868
[13] -0.59076570 3.21582454 1.46389154 2.18139857 -0.81073297 0.91366085
[19] 0.34025996 -0.29069211 0.16053132 1.15328157 -0.18413379 1.49097207
[25] 0.85019058 0.49975473 0.02254259 -1.14038571 -0.11366888 -0.21299747
[31] -0.64761130 0.76845520 2.18328708 -1.15259755 0.76494864 -0.43264619
[37] -1.04034121 -0.81423582 0.55262987 0.16582805 -0.73351240 -0.59687769
[43] 0.09386606 0.07445605 0.14287530 0.47315553 -0.56464216 -0.72948610
[49] -0.67198456 0.51012053 0.71665700 0.18357668 0.24903393 -0.92575091
[55] 0.44106182 -0.71553985 -2.04850844 0.04946201 -0.46343839 0.48855622
[61] -0.67916195 1.65681914 -0.51641031 0.94688443 0.74149074 0.60670684
[67] -0.92248354 -1.50940345 0.11396558 -0.27022434 -0.11619359 -0.23814117
[73] 0.14480153 0.12544927 0.97402258 0.82005646 1.01329028 0.51574488
[79] -0.62734008 0.12352506 0.60822962 -0.25296197 1.76974309 -1.34371710
[85] 0.90558724 1.11478870 -0.54830971 -1.05716697 -1.93140674 0.66382524
[91] -0.63875714 1.52315037 -0.65309526 1.62243612 -0.15394501 -0.08823283
[97] 0.22034360 -0.30656968 1.81138325 -0.04301440
> rowMin(tmp2)
[1] 0.67432711 -0.34875215 -0.64636814 -0.63846120 0.11030333 -0.04132767
[7] -0.04089171 -2.05279164 -0.37694750 0.85364008 -0.06204956 1.57383868
[13] -0.59076570 3.21582454 1.46389154 2.18139857 -0.81073297 0.91366085
[19] 0.34025996 -0.29069211 0.16053132 1.15328157 -0.18413379 1.49097207
[25] 0.85019058 0.49975473 0.02254259 -1.14038571 -0.11366888 -0.21299747
[31] -0.64761130 0.76845520 2.18328708 -1.15259755 0.76494864 -0.43264619
[37] -1.04034121 -0.81423582 0.55262987 0.16582805 -0.73351240 -0.59687769
[43] 0.09386606 0.07445605 0.14287530 0.47315553 -0.56464216 -0.72948610
[49] -0.67198456 0.51012053 0.71665700 0.18357668 0.24903393 -0.92575091
[55] 0.44106182 -0.71553985 -2.04850844 0.04946201 -0.46343839 0.48855622
[61] -0.67916195 1.65681914 -0.51641031 0.94688443 0.74149074 0.60670684
[67] -0.92248354 -1.50940345 0.11396558 -0.27022434 -0.11619359 -0.23814117
[73] 0.14480153 0.12544927 0.97402258 0.82005646 1.01329028 0.51574488
[79] -0.62734008 0.12352506 0.60822962 -0.25296197 1.76974309 -1.34371710
[85] 0.90558724 1.11478870 -0.54830971 -1.05716697 -1.93140674 0.66382524
[91] -0.63875714 1.52315037 -0.65309526 1.62243612 -0.15394501 -0.08823283
[97] 0.22034360 -0.30656968 1.81138325 -0.04301440
>
> colMeans(tmp2)
[1] 0.1039996
> colSums(tmp2)
[1] 10.39996
> colVars(tmp2)
[1] 0.8770364
> colSd(tmp2)
[1] 0.9365022
> colMax(tmp2)
[1] 3.215825
> colMin(tmp2)
[1] -2.052792
> colMedians(tmp2)
[1] 0.06195903
> colRanges(tmp2)
[,1]
[1,] -2.052792
[2,] 3.215825
>
> 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] -4.4266000 2.6055794 0.7610722 -2.6738039 -0.7673036 0.4999436
[7] -3.1378015 -0.6196998 0.4182887 0.6506950
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.7028491
[2,] -1.1673982
[3,] -0.5991558
[4,] 0.1256948
[5,] 1.1284267
>
> rowApply(tmp,sum)
[1] 5.8476273 2.1373756 -3.7256752 -3.6143937 -3.5064656 -1.1428650
[7] -3.8455350 -1.6197560 3.7281864 -0.9481288
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 4 8 5 3 4 5 2 2 9 2
[2,] 9 1 9 9 2 4 10 8 1 8
[3,] 10 7 3 10 1 1 9 10 4 3
[4,] 7 10 1 4 7 3 4 3 6 5
[5,] 6 2 7 7 6 7 6 4 3 6
[6,] 2 6 10 6 3 2 7 9 8 7
[7,] 1 5 4 2 5 6 1 1 10 10
[8,] 5 4 8 5 8 9 8 6 2 1
[9,] 3 9 6 1 9 8 3 7 7 9
[10,] 8 3 2 8 10 10 5 5 5 4
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -1.342770884 1.546321528 -1.388459030 0.743480378 -0.345236222
[6] 0.002152129 0.864885129 -3.896048149 0.185411635 -2.503052665
[11] 1.134935403 -0.733007682 -1.575691467 -3.126630927 -1.807312413
[16] -0.991210721 -0.569096377 -2.275145349 2.303648382 -0.236915278
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.78623318
[2,] -0.37181429
[3,] -0.31125288
[4,] 0.05538260
[5,] 0.07114687
>
> rowApply(tmp,sum)
[1] -10.734988 -2.662321 1.609898 -0.327665 -1.894667
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 13 11 9 5 10
[2,] 4 19 19 4 19
[3,] 1 14 16 8 9
[4,] 16 10 3 18 17
[5,] 11 17 6 11 7
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -0.37181429 -1.0658107 -2.38745549 -0.08279469 -0.43141945 0.7772922
[2,] 0.07114687 0.6971509 0.44032740 0.02475686 0.66031213 -0.6709385
[3,] 0.05538260 1.4989163 0.91940383 -0.94929464 -0.21650015 0.5113112
[4,] -0.78623318 -0.9802125 -0.02989173 0.95059763 0.04394489 0.5405367
[5,] -0.31125288 1.3962776 -0.33084303 0.80021521 -0.40157364 -1.1560495
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.8121915 -1.17247506 -0.03260996 -0.7643791 -0.4983722 -0.3856667
[2,] 0.2209575 -1.91350675 -0.30106241 -0.2809261 0.4894329 0.6836750
[3,] -0.1221357 0.09822240 0.28873007 -2.2445974 1.5414409 0.6886074
[4,] -0.4067743 0.03535961 -1.07280627 0.4347221 1.1404015 -1.3544088
[5,] 0.3606462 -0.94364834 1.30316021 0.3521278 -1.5379677 -0.3652147
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -1.4726584 -0.07614489 -0.93399230 -0.9369132 -0.49966494 -0.2064937
[2,] -0.7574582 -1.26936347 0.26080863 -0.9754720 2.31451556 -1.1216230
[3,] 1.1538774 -0.70654486 -0.08620434 1.4223631 -2.53188874 -0.3755695
[4,] 0.1998103 -1.00289190 0.39308727 0.1443712 -0.01636508 -0.4467762
[5,] -0.6992625 -0.07168580 -1.44101167 -0.6455599 0.16430682 -0.1246830
[,19] [,20]
[1,] -0.8471660 -0.1586402
[2,] 0.5430916 -1.7781459
[3,] 0.2402276 0.4241509
[4,] 0.7373772 1.1484865
[5,] 1.6301181 0.1272334
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.17-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-3.17-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-3.17-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 565 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.17-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 0.5260891 2.030153 0.5243038 2.001077 1.283943 -1.196296 0.217429
col8 col9 col10 col11 col12 col13 col14
row1 0.3211292 1.063886 -0.7693474 1.257646 -1.188719 1.306502 0.7696119
col15 col16 col17 col18 col19 col20
row1 0.6249987 -0.1433048 2.39317 -0.07256963 -0.5952168 -0.4578854
> tmp[,"col10"]
col10
row1 -0.7693474
row2 -1.7565252
row3 0.6846853
row4 -1.4124423
row5 1.0632687
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6
row1 0.5260891 2.0301528 0.5243038 2.0010768 1.2839430 -1.1962957
row5 -0.2707729 -0.6214256 -0.8555853 -0.7418127 -0.9832353 0.1183373
col7 col8 col9 col10 col11 col12 col13
row1 0.2174290 0.3211292 1.063886 -0.7693474 1.2576463 -1.188719 1.3065022
row5 -0.6561836 -0.1859370 -1.883841 1.0632687 -0.7422207 1.466217 0.1122086
col14 col15 col16 col17 col18 col19
row1 0.7696119 0.6249987 -0.143304817 2.3931701 -0.07256963 -0.5952168
row5 -1.5724658 -0.6669892 -0.008492669 0.1438678 -0.23836341 0.5412123
col20
row1 -0.4578854
row5 0.6812998
> tmp[,c("col6","col20")]
col6 col20
row1 -1.1962957 -0.4578854
row2 2.0937198 -0.3827671
row3 0.4824991 0.3668484
row4 0.5576785 -0.5654663
row5 0.1183373 0.6812998
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 -1.1962957 -0.4578854
row5 0.1183373 0.6812998
>
>
>
>
> 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 52.27426 50.1155 51.67394 50.04069 49.10151 104.3558 49.63176 47.39654
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.11255 49.65116 51.60355 50.04325 50.49365 48.88797 50.63274 50.2226
col17 col18 col19 col20
row1 51.00141 49.84468 50.02296 105.3181
> tmp[,"col10"]
col10
row1 49.65116
row2 29.31575
row3 30.53266
row4 28.93957
row5 49.36131
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 52.27426 50.11550 51.67394 50.04069 49.10151 104.3558 49.63176 47.39654
row5 48.94581 51.81363 48.54218 50.85270 51.47247 107.0386 49.16761 48.70556
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.11255 49.65116 51.60355 50.04325 50.49365 48.88797 50.63274 50.22260
row5 50.78842 49.36131 50.08654 51.66069 48.17375 49.83925 51.45935 49.30581
col17 col18 col19 col20
row1 51.00141 49.84468 50.02296 105.3181
row5 49.98902 48.11649 50.13525 104.9861
> tmp[,c("col6","col20")]
col6 col20
row1 104.35576 105.31807
row2 74.62158 74.25416
row3 75.72724 75.53613
row4 73.52703 73.79336
row5 107.03863 104.98608
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 104.3558 105.3181
row5 107.0386 104.9861
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 104.3558 105.3181
row5 107.0386 104.9861
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] 0.2340943
[2,] -0.9008058
[3,] -1.3517986
[4,] 1.6263616
[5,] -0.3229705
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.61791265 0.5021489
[2,] 1.02448521 0.3786541
[3,] 0.91537437 -0.0229861
[4,] 0.51489576 1.4164484
[5,] 0.04860153 -1.1270450
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.4534468 0.8336587
[2,] -0.7580215 0.9544808
[3,] 1.3288789 -0.1999762
[4,] 0.9127693 0.8678055
[5,] -1.6797614 0.1909683
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.4534468
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.4534468
[2,] -0.7580215
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row3 -0.4113487 -1.150650 -0.007556178 0.0162474 -1.354089 0.5474676 2.0844170
row1 -2.0436833 -1.475901 0.416817515 1.8781756 1.584829 0.7851878 -0.4723521
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row3 0.898874 -0.3054156 -1.3649400 -0.7648153 -1.8493511 -1.2778551 0.9631715
row1 1.184050 -0.3235681 0.7281736 -0.5032014 -0.1789245 -0.9971759 0.9555614
[,15] [,16] [,17] [,18] [,19] [,20]
row3 1.7791708 0.5941933 0.7712274 0.08065236 -1.0649111 -0.4543647
row1 -0.5451255 -1.0353609 2.0559491 -0.97481213 -0.7017778 -1.8495523
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 0.9137083 -0.6132775 1.269233 -0.839684 -0.6854677 1.198359 2.094395
[,8] [,9] [,10]
row2 0.8498924 -1.865344 -0.5526448
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 0.007606449 -1.894042 0.02527017 -0.5312601 1.86056 2.229222 1.260861
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 1.503786 -0.08946939 1.024574 0.4329386 -0.1242576 0.2555591 1.453112
[,15] [,16] [,17] [,18] [,19] [,20]
row5 -1.139162 0.6484944 -0.2661859 -1.253562 1.995309 0.3655573
>
>
> 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: 0xaaaae8038ed0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM22fe297a651135"
[2] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM22fe297925fd38"
[3] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM22fe297f44c2af"
[4] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM22fe291749b19b"
[5] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM22fe29337b3d91"
[6] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM22fe299df73d"
[7] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM22fe29844db41"
[8] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM22fe292366c274"
[9] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM22fe2974d3217d"
[10] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM22fe296514dcf5"
[11] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM22fe293dc26d92"
[12] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM22fe297950e774"
[13] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM22fe2945e26629"
[14] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM22fe2913709ec1"
[15] "/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests/BM22fe29243c0a4"
>
>
> ### 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: 0xaaaae65bbb60>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0xaaaae65bbb60>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.17-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0xaaaae65bbb60>
> rowMedians(tmp)
[1] 0.0056017458 0.5508129576 -0.0541118480 0.1997166125 -0.2759447132
[6] 0.5374271010 -0.1674654688 0.0558804843 -0.0642129125 -0.1469900985
[11] 0.0342574502 0.4071477415 0.2477730564 0.1330842235 -0.2952380369
[16] -0.3664106124 0.3436963695 0.2851015003 -0.1924681334 -0.5476531846
[21] 0.0573099587 -0.0004045959 -0.4584388596 0.1603553503 -0.0219371684
[26] 0.5386544464 -0.2918747543 0.2450186026 0.1315439722 0.1214393746
[31] 0.1709554546 -0.2083480919 0.0807731106 -0.0934213637 -0.1018997392
[36] -0.3826948094 -0.0818248659 0.3185897219 0.2276035327 0.0605087667
[41] 0.1488750650 -0.0205393121 1.0008091131 0.0695783418 0.0988970681
[46] -0.2145359903 0.0165860890 -0.5435415080 0.1408784527 0.8968897706
[51] -0.4480509181 0.0317308268 -0.8508307064 0.1196381671 -0.4762007597
[56] 0.0702741950 -0.2389049004 -0.5458564126 0.1883087188 -0.5075851444
[61] 0.6020267298 -0.0869307207 -0.2280902623 0.6279808741 -0.4039520168
[66] 0.0058870385 0.1647775960 -0.5738264920 -0.0488030773 -0.5169346531
[71] 0.0683503548 0.4607885732 0.1929069429 -0.0747771621 -0.0732614998
[76] 0.4292616006 0.9491082226 -0.0140699226 -0.4182162664 -0.1515480913
[81] 0.8753774690 -0.0410043780 -0.3823257386 0.1392988755 -0.3460274244
[86] -0.3143556235 0.3330024333 -0.2754902063 -0.6144919546 0.0653921475
[91] -0.0232772284 -0.4502273057 -0.0981150407 -0.2566120524 -0.2583330553
[96] 0.3141713255 -0.0415170325 0.0628593566 0.2388768821 -0.2620968253
[101] -0.3786662261 -0.6322680104 0.4105641248 -0.8116239293 0.4086614320
[106] 0.0322505046 0.0170299479 -0.1457026814 0.2224851386 -0.0930277013
[111] -0.2035788187 -0.3115716362 0.1626847243 0.2765942073 0.4393722148
[116] -0.3353812419 0.4208033552 -0.0732530856 0.1851955961 -0.1802709841
[121] -0.3257108062 0.1602458352 0.0404088713 -0.2176036029 0.3245944771
[126] 0.1166290144 0.0682698453 0.2227444720 -0.5835707838 0.0023700824
[131] -0.0732844614 -0.2428954746 -0.6329674927 -0.0800651711 0.1090597573
[136] 0.6877154737 0.0034038322 -0.0383014128 -0.2025802760 -0.0939066675
[141] 0.3933241115 -0.2772743323 -0.4238682485 0.4711519717 0.0304853235
[146] 0.7366870589 -0.1165041141 0.1674468246 0.1682713090 -0.3100334624
[151] -0.0147270468 -0.6085218321 -0.2227012808 0.3300683860 -0.1632654681
[156] 0.0226849164 0.3777301342 0.0131281615 0.3416823157 0.0103516729
[161] -0.2968021170 -0.2471252048 0.1927953497 0.5717408706 0.1085599336
[166] 0.6804499320 -0.4118488470 -0.0768229246 0.1040411919 0.1033867545
[171] -0.0854792054 0.2915980423 -0.2538817814 -0.4275866423 -0.0571019878
[176] 0.2595396134 0.4123765539 -0.3003492257 0.3728329065 0.1961671367
[181] 0.1461464234 -0.4072324402 -0.4625255383 0.4349405268 0.1728195819
[186] -0.2073506102 0.5688351103 0.1674512602 -0.1403647736 0.5138242314
[191] -0.0793949939 -0.2400681217 0.3765846556 -0.3646735484 -0.1481016737
[196] -0.1244819102 -0.1556418154 -0.2496999254 -0.4862114049 -0.4832249450
[201] 0.0479856855 0.0658959478 0.1953923031 0.5200056624 0.0323892244
[206] 0.2527509494 -0.2513646446 0.3267707069 -0.2186745753 -0.2123575090
[211] 0.2209150903 -0.4003981956 -0.0333416579 -0.1655643350 -0.1895859745
[216] -0.1448072853 0.6315181995 0.1074816302 -0.1649450272 0.3688073730
[221] -0.2904657955 0.0756786035 0.8087682808 0.1839429486 0.1578608258
[226] 0.3353322458 -0.0695882770 -0.3261520039 0.3190272383 -0.1685733687
>
> proc.time()
user system elapsed
1.998 1.206 3.245
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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: 0xaaaafbf0e8e0>
> .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: 0xaaaafbf0e8e0>
> .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: 0xaaaafbf0e8e0>
> .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: 0xaaaafbf0e8e0>
> 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: 0xaaaafc6cf270>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaafc6cf270>
> .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: 0xaaaafc6cf270>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaafc6cf270>
> .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: 0xaaaafc6cf270>
> 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: 0xaaaafbebcdc0>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaafbebcdc0>
> .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: 0xaaaafbebcdc0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0xaaaafbebcdc0>
> .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: 0xaaaafbebcdc0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0xaaaafbebcdc0>
> .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: 0xaaaafbebcdc0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0xaaaafbebcdc0>
> .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: 0xaaaafbebcdc0>
> 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: 0xaaaafc73a370>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0xaaaafc73a370>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaafc73a370>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaafc73a370>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile22fe3c4344d70b" "BufferedMatrixFile22fe3c55067fc6"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile22fe3c4344d70b" "BufferedMatrixFile22fe3c55067fc6"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaafe073980>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaafe073980>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0xaaaafe073980>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0xaaaafe073980>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0xaaaafe073980>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0xaaaafe073980>
> .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: 0xaaaafdb49fe0>
> .Call("R_bm_AddColumn",P)
<pointer: 0xaaaafdb49fe0>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0xaaaafdb49fe0>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0xaaaafdb49fe0>
> 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: 0xaaaafe07f500>
> .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: 0xaaaafe07f500>
> rm(P)
>
> proc.time()
user system elapsed
0.332 0.045 0.363
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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.
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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
0.348 0.038 0.371