Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:29:30 -0400 (Wed, 17 Oct 2018).
Package 583/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
geneXtendeR 1.6.0 Bohdan Khomtchouk
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: geneXtendeR |
Version: 1.6.0 |
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings geneXtendeR_1.6.0.tar.gz |
StartedAt: 2018-10-16 00:41:44 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 00:50:52 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 547.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: geneXtendeR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:geneXtendeR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings geneXtendeR_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/geneXtendeR.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘geneXtendeR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘geneXtendeR’ version ‘1.6.0’ * 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 ‘geneXtendeR’ can be installed ... OK * checking installed package size ... NOTE installed size is 7.4Mb sub-directories of 1Mb or more: data 5.8Mb extdata 1.2Mb * 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 ... NOTE Namespaces in Imports field not imported from: ‘RColorBrewer’ ‘SnowballC’ ‘networkD3’ ‘org.Ag.eg.db’ ‘org.Bt.eg.db’ ‘org.Ce.eg.db’ ‘org.Cf.eg.db’ ‘org.Dm.eg.db’ ‘org.Dr.eg.db’ ‘org.Gg.eg.db’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ ‘org.Mmu.eg.db’ ‘org.Pt.eg.db’ ‘org.Sc.sgd.db’ ‘org.Ss.eg.db’ ‘org.Xl.eg.db’ ‘wordcloud’ All declared Imports should be used. Packages in Depends field not imported from: ‘GO.db’ ‘org.Rn.eg.db’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE annotate : geneXtender: no visible binding for global variable ‘type’ annotate : geneXtender: no visible binding for global variable ‘seqid’ annotate : geneXtender: no visible binding for global variable ‘gene_id’ annotate : geneXtender: no visible binding for global variable ‘gene_name’ barChart : geneXtender: no visible binding for global variable ‘type’ barChart : geneXtender: no visible binding for global variable ‘seqid’ barChart : geneXtender: no visible binding for global variable ‘gene_id’ barChart : geneXtender: no visible binding for global variable ‘gene_name’ cumlinePlot : geneXtender: no visible binding for global variable ‘type’ cumlinePlot : geneXtender: no visible binding for global variable ‘seqid’ cumlinePlot : geneXtender: no visible binding for global variable ‘gene_id’ cumlinePlot : geneXtender: no visible binding for global variable ‘gene_name’ diffGO : geneXtender: no visible binding for global variable ‘type’ diffGO : geneXtender: no visible binding for global variable ‘seqid’ diffGO : geneXtender: no visible binding for global variable ‘gene_id’ diffGO : geneXtender: no visible binding for global variable ‘gene_name’ diffGO: no visible binding for global variable ‘GO.db’ distinct : geneXtender: no visible binding for global variable ‘type’ distinct : geneXtender: no visible binding for global variable ‘seqid’ distinct : geneXtender: no visible binding for global variable ‘gene_id’ distinct : geneXtender: no visible binding for global variable ‘gene_name’ hotspotPlot : geneXtender: no visible binding for global variable ‘type’ hotspotPlot : geneXtender: no visible binding for global variable ‘seqid’ hotspotPlot : geneXtender: no visible binding for global variable ‘gene_id’ hotspotPlot : geneXtender: no visible binding for global variable ‘gene_name’ linePlot : geneXtender: no visible binding for global variable ‘type’ linePlot : geneXtender: no visible binding for global variable ‘seqid’ linePlot : geneXtender: no visible binding for global variable ‘gene_id’ linePlot : geneXtender: no visible binding for global variable ‘gene_name’ makeNetwork : geneXtender: no visible binding for global variable ‘type’ makeNetwork : geneXtender: no visible binding for global variable ‘seqid’ makeNetwork : geneXtender: no visible binding for global variable ‘gene_id’ makeNetwork : geneXtender: no visible binding for global variable ‘gene_name’ makeNetwork: no visible binding for global variable ‘GO.db’ makeNetwork: no visible global function definition for ‘%>%’ makeNetwork: no visible global function definition for ‘left_join’ makeNetwork: no visible global function definition for ‘rename’ makeNetwork: no visible binding for global variable ‘id’ makeNetwork: no visible global function definition for ‘forceNetwork’ makeNetwork: no visible global function definition for ‘JS’ makeWordCloud : geneXtender: no visible binding for global variable ‘type’ makeWordCloud : geneXtender: no visible binding for global variable ‘seqid’ makeWordCloud : geneXtender: no visible binding for global variable ‘gene_id’ makeWordCloud : geneXtender: no visible binding for global variable ‘gene_name’ makeWordCloud: no visible binding for global variable ‘GO.db’ makeWordCloud: no visible global function definition for ‘VectorSource’ makeWordCloud: no visible binding for global variable ‘removeWords’ makeWordCloud: no visible global function definition for ‘stopwords’ makeWordCloud: no visible global function definition for ‘wordcloud’ makeWordCloud: no visible global function definition for ‘brewer.pal’ meanPeakLength : geneXtender: no visible binding for global variable ‘type’ meanPeakLength : geneXtender: no visible binding for global variable ‘seqid’ meanPeakLength : geneXtender: no visible binding for global variable ‘gene_id’ meanPeakLength : geneXtender: no visible binding for global variable ‘gene_name’ peaksInput: no visible binding for global variable ‘chr’ peaksMerge: no visible binding for global variable ‘chr’ peaksMerge: no visible binding for global variable ‘g’ peaksMerge: no visible global function definition for ‘.’ plotWordFreq : geneXtender: no visible binding for global variable ‘type’ plotWordFreq : geneXtender: no visible binding for global variable ‘seqid’ plotWordFreq : geneXtender: no visible binding for global variable ‘gene_id’ plotWordFreq : geneXtender: no visible binding for global variable ‘gene_name’ plotWordFreq: no visible binding for global variable ‘GO.db’ plotWordFreq: no visible global function definition for ‘VectorSource’ plotWordFreq: no visible binding for global variable ‘removeWords’ plotWordFreq: no visible global function definition for ‘stopwords’ Undefined global functions or variables: %>% . GO.db JS VectorSource brewer.pal chr forceNetwork g gene_id gene_name id left_join removeWords rename seqid stopwords type wordcloud * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... 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 ... OK Examples with CPU or elapsed time > 5s user system elapsed meanPeakLengthPlot 30.224 0.196 59.123 hotspotPlot 23.208 0.216 37.254 linePlot 17.024 0.164 20.205 barChart 16.532 0.228 19.770 cumlinePlot 15.236 0.172 18.783 makeNetwork 14.048 0.200 45.202 annotate 14.052 0.164 17.045 makeWordCloud 13.648 0.192 48.819 diffGO 11.848 0.100 15.072 plotWordFreq 11.256 0.272 22.192 meanPeakLength 10.700 0.104 15.830 distinct 10.700 0.072 18.533 peakLengthBoxplot 10.364 0.120 29.280 * 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.7-bioc/meat/geneXtendeR.Rcheck/00check.log’ for details.
geneXtendeR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL geneXtendeR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘geneXtendeR’ ... ** libs gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c annotate.c -o annotate.o annotate.c: In function ‘annotate’: annotate.c:106:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(varstr, 50000, varfp); ^ annotate.c:116:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(vcfstr, 10000, vcffp); ^ gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c extract_number.c -o extract_number.o extract_number.c: In function ‘extractnumber’: extract_number.c:72:10: warning: variable ‘n_1’ set but not used [-Wunused-but-set-variable] long n_1; ^ extract_number.c:66:10: warning: variable ‘j_1’ set but not used [-Wunused-but-set-variable] long j_1; ^ extract_number.c:54:12: warning: variable ‘pvcfcol5_5’ set but not used [-Wunused-but-set-variable] char * pvcfcol5_5; ^ extract_number.c:53:12: warning: variable ‘pvcfcol4_4’ set but not used [-Wunused-but-set-variable] char * pvcfcol4_4; ^ extract_number.c:52:12: warning: variable ‘pvcfcol3_3’ set but not used [-Wunused-but-set-variable] char * pvcfcol3_3; ^ extract_number.c:51:12: warning: variable ‘pvcfcol2_2’ set but not used [-Wunused-but-set-variable] char * pvcfcol2_2; ^ extract_number.c:50:12: warning: variable ‘pvcfcol1_1’ set but not used [-Wunused-but-set-variable] char * pvcfcol1_1; ^ extract_number.c:98:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(varstr, 50000, varfp); ^ extract_number.c:108:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(vcfstr, 10000, vcffp); ^ gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c extract_peaks.c -o extract_peaks.o extract_peaks.c: In function ‘extractpeaks’: extract_peaks.c:107:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(varstr, 50000, varfp); ^ extract_peaks.c:117:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(vcfstr, 10000, vcffp); ^ gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o geneXtendeR.so annotate.o extract_number.o extract_peaks.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.7-bioc/R/library/geneXtendeR/libs ** R ** data *** moving datasets to lazyload DB ** 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 * DONE (geneXtendeR)
geneXtendeR.Rcheck/geneXtendeR-Ex.timings
name | user | system | elapsed | |
allPeakLengths | 0.016 | 0.004 | 0.043 | |
annotate | 14.052 | 0.164 | 17.045 | |
barChart | 16.532 | 0.228 | 19.770 | |
cumlinePlot | 15.236 | 0.172 | 18.783 | |
diffGO | 11.848 | 0.100 | 15.072 | |
distinct | 10.700 | 0.072 | 18.533 | |
hotspotPlot | 23.208 | 0.216 | 37.254 | |
linePlot | 17.024 | 0.164 | 20.205 | |
makeNetwork | 14.048 | 0.200 | 45.202 | |
makeWordCloud | 13.648 | 0.192 | 48.819 | |
meanPeakLength | 10.700 | 0.104 | 15.830 | |
meanPeakLengthPlot | 30.224 | 0.196 | 59.123 | |
peakLengthBoxplot | 10.364 | 0.120 | 29.280 | |
peaksInput | 0.292 | 0.096 | 0.641 | |
peaksMerge | 0.212 | 0.012 | 0.217 | |
plotWordFreq | 11.256 | 0.272 | 22.192 | |
rat | 2.620 | 0.172 | 2.794 | |
samplepeaksinput | 0.008 | 0.000 | 0.007 | |