BioC 3.5: CHECK report for geneXtendeR on veracruz2
This page was generated on 2017-08-16 13:35:06 -0400 (Wed, 16 Aug 2017).
geneXtendeR 1.2.0 Bohdan Khomtchouk
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/geneXtendeR | Last Changed Rev: 129126 / Revision: 131943 | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK |  |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK |  |
Summary
Package: geneXtendeR |
Version: 1.2.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings geneXtendeR_1.2.0.tar.gz |
StartedAt: 2017-08-16 03:16:22 -0400 (Wed, 16 Aug 2017) |
EndedAt: 2017-08-16 03:21:59 -0400 (Wed, 16 Aug 2017) |
EllapsedTime: 337.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: geneXtendeR.Rcheck |
Warnings: 0 |
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings geneXtendeR_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/geneXtendeR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.2.0’
* 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 6.7Mb
sub-directories of 1Mb or more:
data 5.8Mb
* 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 ... 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’
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’
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’
peaksInput: no visible binding for global variable ‘chr’
Undefined global functions or variables:
chr gene_id gene_name seqid type
* 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 sizes of PDF files under ‘inst/doc’ ... 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
linePlot 23.811 1.914 29.858
barChart 23.613 1.776 29.601
annotate 16.398 0.427 20.686
distinct 14.598 0.618 18.981
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/geneXtendeR.Rcheck/00check.log’
for details.
geneXtendeR.Rcheck/00install.out:
* installing *source* package ‘geneXtendeR’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c annotate.c -o annotate.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c extract_number.c -o extract_number.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c extract_peaks.c -o extract_peaks.o
clang -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 geneXtendeR.so annotate.o extract_number.o extract_peaks.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-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)
geneXtendeR.Rcheck/geneXtendeR-Ex.timings:
name | user | system | elapsed
|
annotate | 16.398 | 0.427 | 20.686 |
|
barChart | 23.613 | 1.776 | 29.601 |
|
distinct | 14.598 | 0.618 | 18.981 |
|
linePlot | 23.811 | 1.914 | 29.858 |
|
peaksInput | 0.221 | 0.024 | 0.262 |
|
rat | 4.138 | 0.336 | 4.656 |
|
samplepeaksinput | 0.009 | 0.000 | 0.010 |
|