Alex Chit Hei Wong
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/ompBAM |
| git_branch: RELEASE_3_16 |
| git_last_commit: 221f468 |
| git_last_commit_date: 2022-11-01 11:26:57 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:18 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 ompBAM package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ompBAM.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 1394/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ompBAM 1.2.0 (landing page) Alex Chit Hei Wong
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ompBAM |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ompBAM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ompBAM_1.2.0.tar.gz |
| StartedAt: 2023-04-10 21:37:40 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 21:38:35 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 54.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ompBAM.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ompBAM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ompBAM_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/ompBAM.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ompBAM/DESCRIPTION’ ... OK
* this is package ‘ompBAM’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘ompBAM’ can be installed ... OK
* 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
install_ompBAM_example 9.338 1.68 12.419
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
ompBAM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ompBAM ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘ompBAM’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ompBAM)
ompBAM.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(testthat)
> library(ompBAM)
>
> test_check("ompBAM")
i Loading ompBAMExample
Exports from /private/tmp/RtmpZyAvIf/file1550238cd41f8/ompBAMExample/src/main.cpp:
int idxstats_pbam(std::string bam_file, int n_threads_to_use = 1, bool verbose = true)
/private/tmp/RtmpZyAvIf/file1550238cd41f8/ompBAMExample/src/RcppExports.cpp updated.
/private/tmp/RtmpZyAvIf/file1550238cd41f8/ompBAMExample/R/RcppExports.R updated.
i Re-compiling ompBAMExample (debug build)
-- R CMD INSTALL ---------------------------------------------------------------
* installing *source* package ‘ompBAMExample’ ...
** using staged installation
Configuring without OpenMP for MacOS
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ompBAM/include' -I/usr/local/include -fPIC -Wall -g -O2 -UNDEBUG -Wall -pedantic -g -O0 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ompBAM/include' -I/usr/local/include -fPIC -Wall -g -O2 -UNDEBUG -Wall -pedantic -g -O0 -c main.cpp -o main.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ompBAMExample.so RcppExports.o main.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /private/tmp/RtmpZyAvIf/devtools_install_15502644b4fbf/00LOCK-ompBAMExample/00new/ompBAMExample/libs
** checking absolute paths in shared objects and dynamic libraries
* DONE (ompBAMExample)
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ompBAM/extdata/THP1_ND_1.bam summary:
Name Length Number of reads
1 248956422 1308
10 133797422 308
11 135086622 600
12 133275309 648
13 114364328 162
14 107043718 230
15 101991189 294
16 90338345 334
17 83257441 570
18 80373285 78
19 58617616 600
2 242193529 586
20 64444167 168
21 46709983 76
22 50818468 200
3 198295559 454
4 190214555 252
5 181538259 516
6 170805979 824
7 159345973 412
8 145138636 452
9 138394717 372
MT 16569 288
X 156040895 254
Y 57227415 14
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ompBAM/extdata/MGE_E35_1.bam summary:
Name Length Number of reads
1 195471971 50000
10 130694993 0
11 122082543 0
12 120129022 0
13 120421639 0
14 124902244 0
15 104043685 0
16 98207768 0
17 94987271 0
18 90702639 0
19 61431566 0
2 182113224 0
3 160039680 0
4 156508116 0
5 151834684 0
6 149736546 0
7 145441459 0
8 129401213 0
9 124595110 0
MT 16299 0
X 171031299 0
Y 91744698 0
JH584299.1 953012 0
GL456233.1 336933 0
JH584301.1 259875 0
GL456211.1 241735 0
GL456350.1 227966 0
JH584293.1 207968 0
GL456221.1 206961 0
JH584297.1 205776 0
JH584296.1 199368 0
GL456354.1 195993 0
JH584294.1 191905 0
JH584298.1 184189 0
JH584300.1 182347 0
GL456219.1 175968 0
GL456210.1 169725 0
JH584303.1 158099 0
JH584302.1 155838 0
GL456212.1 153618 0
JH584304.1 114452 0
GL456379.1 72385 0
GL456216.1 66673 0
GL456393.1 55711 0
GL456366.1 47073 0
GL456367.1 42057 0
GL456239.1 40056 0
GL456213.1 39340 0
GL456383.1 38659 0
GL456385.1 35240 0
GL456360.1 31704 0
GL456378.1 31602 0
GL456389.1 28772 0
GL456372.1 28664 0
GL456370.1 26764 0
GL456381.1 25871 0
GL456387.1 24685 0
GL456390.1 24668 0
GL456394.1 24323 0
GL456392.1 23629 0
GL456382.1 23158 0
GL456359.1 22974 0
GL456396.1 21240 0
GL456368.1 20208 0
JH584292.1 14945 0
JH584295.1 1976 0
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
>
> proc.time()
user system elapsed
9.804 1.693 12.589
ompBAM.Rcheck/ompBAM-Ex.timings
| name | user | system | elapsed | |
| example_BAM | 0.001 | 0.001 | 0.001 | |
| install_ompBAM_example | 9.338 | 1.680 | 12.419 | |
| use_ompBAM | 0.414 | 0.049 | 0.468 | |