Jitao David Zhang
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/BioQC |
| git_branch: RELEASE_3_17 |
| git_last_commit: 717b921 |
| git_last_commit_date: 2023-04-25 10:42:59 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:13 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 214/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BioQC 1.28.0 (landing page) Jitao David Zhang
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the BioQC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioQC.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BioQC |
| Version: 1.28.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BioQC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BioQC_1.28.0.tar.gz |
| StartedAt: 2023-10-15 19:37:51 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 19:40:27 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 156.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BioQC.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BioQC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BioQC_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BioQC.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BioQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioQC’ version ‘1.28.0’
* 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 ‘BioQC’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 ...
‘BioQC.Rmd’ using ‘UTF-8’... OK
‘bioqc-efficiency.Rmd’ using ‘UTF-8’... OK
‘bioqc-introduction.Rmd’ using ‘UTF-8’... OK
‘bioqc-signedGenesets.Rmd’ using ‘UTF-8’... OK
‘bioqc-simulation.Rmd’ using ‘UTF-8’... OK
‘bioqc-wmw-test-performance.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/BioQC.Rcheck/00check.log’
for details.
BioQC.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BioQC
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘BioQC’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c gini.c -o gini.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c read_gmt.cpp -o read_gmt.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c stat_rank.c -o stat_rank.o
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.17-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c wmw_test.c -o wmw_test.o
wmw_test.c: In function ‘wmw_test_list’:
wmw_test.c:118: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
118 | #pragma omp parallel for
|
wmw_test.c: In function ‘wmw_test’:
wmw_test.c:168: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
168 | #pragma omp parallel for
|
wmw_test.c: In function ‘signed_wmw_test_list’:
wmw_test.c:201: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
201 | #pragma omp parallel for
|
wmw_test.c: In function ‘signed_wmw_test’:
wmw_test.c:270: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
270 | #pragma omp parallel for
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g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o BioQC.so gini.o init.o read_gmt.o stat_rank.o wmw_test.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-BioQC/00new/BioQC/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (BioQC)
BioQC.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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(testthat)
> library(BioQC)
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> test_check("BioQC")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 125 ]
>
> proc.time()
user system elapsed
7.562 0.221 7.774
BioQC.Rcheck/BioQC-Ex.timings
| name | user | system | elapsed | |
| GmtList | 0.002 | 0.000 | 0.002 | |
| IndexList | 0.004 | 0.000 | 0.004 | |
| SignedGenesets | 0.001 | 0.000 | 0.001 | |
| SignedIndexList | 0.000 | 0.002 | 0.002 | |
| absLog10p | 0.000 | 0.000 | 0.001 | |
| appendGmtList | 0.004 | 0.000 | 0.004 | |
| as.GmtList | 0.000 | 0.000 | 0.001 | |
| entropy | 0.001 | 0.000 | 0.002 | |
| entropyDiversity | 0.004 | 0.000 | 0.004 | |
| entropySpecificity | 0.005 | 0.000 | 0.005 | |
| filterPmat | 0.002 | 0.000 | 0.002 | |
| getLeadingEdgeIndexFromVector | 0.003 | 0.000 | 0.003 | |
| gini | 0.001 | 0.000 | 0.001 | |
| gmtlist2signedGenesets | 0.004 | 0.000 | 0.004 | |
| matchGenes | 0.083 | 0.004 | 0.087 | |
| offset-set | 0.001 | 0.000 | 0.002 | |
| offset | 0.001 | 0.000 | 0.001 | |
| prettySigNames | 0.069 | 0.000 | 0.070 | |
| readCurrentSignatures | 0.042 | 0.000 | 0.042 | |
| readGmt | 0.059 | 0.000 | 0.060 | |
| readSignedGmt | 0.007 | 0.000 | 0.006 | |
| sampleSpecialization | 0.002 | 0.004 | 0.005 | |
| setNamespace | 0.006 | 0.000 | 0.005 | |
| simplifyMatrix | 0.001 | 0.000 | 0.001 | |
| sub-.GmtList | 0.001 | 0.000 | 0.002 | |
| sub-sub-.GmtList | 0.001 | 0.000 | 0.000 | |
| uniqGenesetsByNamespace | 0.006 | 0.000 | 0.005 | |
| wmwLeadingEdge | 0.013 | 0.000 | 0.012 | |
| wmwTest | 0.184 | 0.000 | 0.183 | |
| wmwTestInR | 0.004 | 0.000 | 0.004 | |