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BioC 3.5: CHECK report for GOsummaries on toluca2

This page was generated on 2017-04-23 14:38:58 -0400 (Sun, 23 Apr 2017).

Package 580/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOsummaries 2.9.0
Raivo Kolde
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GOsummaries
Last Changed Rev: 122712 / Revision: 129046
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GOsummaries
Version: 2.9.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOsummaries_2.9.0.tar.gz
StartedAt: 2017-04-23 04:53:25 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 04:54:16 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 51.0 seconds
RetCode: 0
Status:  OK 
CheckDir: GOsummaries.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GOsummaries_2.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GOsummaries.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOsummaries/DESCRIPTION’ ... OK
* this is package ‘GOsummaries’ version ‘2.9.0’
* 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 ‘GOsummaries’ can be installed ... OK
* 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 ... NOTE
adjust_wordcloud_appearance: no visible global function definition for
  ‘colorRampPalette’
annotate.gosummaries: no visible global function definition for
  ‘packageVersion’
gen_wordcloud_legend: no visible global function definition for
  ‘colorRampPalette’
open_file_con : <anonymous>: no visible global function definition for
  ‘pdf’
open_file_con : <anonymous>: no visible global function definition for
  ‘png’
open_file_con : <anonymous>: no visible global function definition for
  ‘jpeg’
open_file_con : <anonymous>: no visible global function definition for
  ‘tiff’
open_file_con : <anonymous>: no visible global function definition for
  ‘bmp’
panel_boxplot : qq: no visible global function definition for
  ‘boxplot.stats’
panel_boxplot: no visible binding for global variable ‘x’
panel_boxplot: no visible binding for global variable ‘y’
panel_boxplot: no visible binding for global variable ‘Class’
panel_dummy: no visible binding for global variable ‘y’
panel_dummy: no visible binding for global variable ‘x’
plotWordcloud: no visible global function definition for
  ‘colorRampPalette’
plotWordcloud: no visible global function definition for ‘runif’
plot_motor: no visible global function definition for ‘dev.off’
print.gosummaries: no visible global function definition for ‘head’
pspearman: no visible global function definition for ‘pt’
spearman_mds: no visible global function definition for ‘cor’
Undefined global functions or variables:
  Class bmp boxplot.stats colorRampPalette cor dev.off head jpeg
  packageVersion pdf png pt runif tiff x y
Consider adding
  importFrom("grDevices", "bmp", "boxplot.stats", "colorRampPalette",
             "dev.off", "jpeg", "pdf", "png", "tiff")
  importFrom("stats", "cor", "pt", "runif")
  importFrom("utils", "head", "packageVersion")
to your NAMESPACE file.
* 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 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 ... 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
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘BiocStyle’
* 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/GOsummaries.Rcheck/00check.log’
for details.


GOsummaries.Rcheck/00install.out:

* installing *source* package ‘GOsummaries’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c findCoordinates.cpp -o findCoordinates.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 GOsummaries.so findCoordinates.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/GOsummaries.Rcheck/GOsummaries/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GOsummaries)

GOsummaries.Rcheck/GOsummaries-Ex.timings:

nameusersystemelapsed
add_expression.gosummaries0.0010.0000.001
add_to_slot.gosummaries0.3380.0070.354
customize0.0000.0000.001
gosummaries.MArrayLM0.0020.0000.001
gosummaries1.7820.0181.807
gosummaries.kmeans0.0010.0000.000
gosummaries.matrix0.0010.0010.001
gosummaries.prcomp3.4920.0123.526
panel_boxplot0.0010.0000.001
plot.gosummaries0.0010.0000.002
plotWordcloud0.1810.0080.192