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This page was generated on 2023-04-12 11:06:18 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (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

CHECK results for ompBAM on lconway


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.

raw results

Package 1394/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ompBAM 1.2.0  (landing page)
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)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

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

Command output

##############################################################################
##############################################################################
###
### 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


Installation output

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)

Tests output

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 

Example timings

ompBAM.Rcheck/ompBAM-Ex.timings

nameusersystemelapsed
example_BAM0.0010.0010.001
install_ompBAM_example 9.338 1.68012.419
use_ompBAM0.4140.0490.468