geneXtendeR 1.3.5
Bohdan Khomtchouk
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/geneXtendeR | | Last Changed Rev: 131878 / Revision: 131943 | | Last Changed Date: 2017-08-09 20:38:47 -0400 (Wed, 09 Aug 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings geneXtendeR_1.3.5.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/geneXtendeR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.3.5’
* 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 8.0Mb
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 loading without being on the library search path ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
meanPeakLengthPlot 36.900 0.204 39.721
hotspotPlot 29.628 0.228 32.576
barChart 20.016 0.296 22.749
cumlinePlot 19.172 0.152 21.916
linePlot 18.984 0.204 22.209
annotate 15.052 0.508 19.078
diffGO 12.632 0.196 15.565
makeWordCloud 12.656 0.124 15.828
makeNetwork 11.688 0.152 14.604
plotWordFreq 11.420 0.284 14.378
peakLengthBoxplot 11.044 0.200 13.795
distinct 10.992 0.136 14.232
meanPeakLength 9.996 0.092 13.459
* 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 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/geneXtendeR.Rcheck/00check.log’
for details.
* installing *source* package ‘geneXtendeR’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-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-3.6-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-3.6-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-3.6-bioc/R/lib -L/usr/local/lib -o geneXtendeR.so annotate.o extract_number.o extract_peaks.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/geneXtendeR.Rcheck/geneXtendeR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (geneXtendeR)