Jitao David Zhang
| Snapshot Date: 2019-09-30 17:00:39 -0400 (Mon, 30 Sep 2019) |
| URL: https://git.bioconductor.org/packages/BioQC |
| Branch: RELEASE_3_9 |
| Last Commit: 54cb13d |
| Last Changed Date: 2019-05-02 11:53:59 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-01 12:50:09 -0400 (Tue, 01 Oct 2019).
| Package 166/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BioQC 1.12.0 Jitao David Zhang
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: BioQC |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BioQC.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BioQC_1.12.0.tar.gz |
| StartedAt: 2019-09-30 23:51:48 -0400 (Mon, 30 Sep 2019) |
| EndedAt: 2019-09-30 23:52:31 -0400 (Mon, 30 Sep 2019) |
| EllapsedTime: 43.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BioQC.Rcheck |
| Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BioQC.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BioQC_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BioQC.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BioQC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BioQC’ version ‘1.12.0’ * 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 ‘BioQC’ can be installed ... WARNING Found the following significant warnings: Warning: /home/biocbuild/bbs-3.9-bioc/meat/BioQC/man/IndexList.Rd:6: All text must be in a section Warning: /home/biocbuild/bbs-3.9-bioc/meat/BioQC/man/IndexList.Rd:7: All text must be in a section Warning: /home/biocbuild/bbs-3.9-bioc/meat/BioQC/man/IndexList.Rd:9: All text must be in a section See ‘/home/biocbuild/bbs-3.9-bioc/meat/BioQC.Rcheck/00install.out’ for details. * 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 ... WARNING prepare_Rd: IndexList.Rd:6: All text must be in a section prepare_Rd: IndexList.Rd:7: All text must be in a section prepare_Rd: IndexList.Rd:9: All text must be in a section * 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 ... WARNING Bad \usage lines found in documentation object 'IndexList': <<<<<<< HEAD ======= >>>>>>> db884caed21e4f2384482a3834c89b269eaa7cc6 Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 1 NOTE See ‘/home/biocbuild/bbs-3.9-bioc/meat/BioQC.Rcheck/00check.log’ for details.
BioQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BioQC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘BioQC’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.9-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I/usr/local/include -fpic -g -O2 -Wall -c gini.c -o gini.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.9-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.9-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I/usr/local/include -fpic -g -O2 -Wall -c read_gmt.cpp -o read_gmt.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.9-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I/usr/local/include -fpic -g -O2 -Wall -c stat_rank.c -o stat_rank.o gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.9-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -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:105:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for wmw_test.c: In function ‘wmw_test’: wmw_test.c:155:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for wmw_test.c: In function ‘signed_wmw_test_list’: wmw_test.c:188:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for wmw_test.c: In function ‘signed_wmw_test’: wmw_test.c:257:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas] #pragma omp parallel for g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-BioQC/00new/BioQC/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help Warning: /home/biocbuild/bbs-3.9-bioc/meat/BioQC/man/IndexList.Rd:6: All text must be in a section Warning: /home/biocbuild/bbs-3.9-bioc/meat/BioQC/man/IndexList.Rd:7: All text must be in a section Warning: /home/biocbuild/bbs-3.9-bioc/meat/BioQC/man/IndexList.Rd:9: All text must be in a section *** 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 (BioQC)
BioQC.Rcheck/tests/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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: Rcpp
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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, 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")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 99 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
9.035 0.108 9.145
BioQC.Rcheck/BioQC-Ex.timings
| name | user | system | elapsed | |
| GmtList | 0.003 | 0.000 | 0.003 | |
| IndexList | 0.006 | 0.000 | 0.007 | |
| SignedGenesets | 0.000 | 0.001 | 0.001 | |
| SignedIndexList | 0.001 | 0.002 | 0.002 | |
| absLog10p | 0.001 | 0.000 | 0.001 | |
| as.gmtlist | 0.000 | 0.000 | 0.001 | |
| entropy | 0.008 | 0.004 | 0.013 | |
| filterPmat | 0.001 | 0.000 | 0.001 | |
| gini | 0.000 | 0.000 | 0.001 | |
| gmtlist2signedGenesets | 0.003 | 0.000 | 0.004 | |
| offset-BaseIndexList-method | 0.001 | 0.000 | 0.001 | |
| offset-set | 0.001 | 0.000 | 0.001 | |
| readGmt | 0.02 | 0.00 | 0.04 | |
| readSignedGmt | 0.002 | 0.004 | 0.006 | |
| simplifyMatrix | 0 | 0 | 0 | |
| wmwTest | 0.217 | 0.008 | 0.226 | |
| wmwTestInR | 0.006 | 0.000 | 0.005 | |