BioC 3.5: CHECK report for TargetSearch on toluca2
This page was generated on 2017-04-23 14:34:49 -0400 (Sun, 23 Apr 2017).
TargetSearch 1.31.0 Alvaro Cuadros-Inostroza
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TargetSearch | 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 | OK | OK | OK | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
Summary
Package: TargetSearch |
Version: 1.31.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TargetSearch_1.31.0.tar.gz |
StartedAt: 2017-04-23 10:37:42 -0400 (Sun, 23 Apr 2017) |
EndedAt: 2017-04-23 10:39:18 -0400 (Sun, 23 Apr 2017) |
EllapsedTime: 95.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TargetSearch.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TargetSearch_1.31.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TargetSearch.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 ‘TargetSearch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TargetSearch’ version ‘1.31.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘TargetSearch’ 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 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
ProfileCleanUp: no visible global function definition for ‘as.dist’
plotPeak: no visible global function definition for ‘mtext’
plotPeak: no visible global function definition for ‘rect’
plotPeak: no visible global function definition for ‘gray’
plotPeak: no visible global function definition for ‘matlines’
Undefined global functions or variables:
as.dist gray matlines mtext rect
Consider adding
importFrom("grDevices", "gray")
importFrom("graphics", "matlines", "mtext", "rect")
importFrom("stats", "as.dist")
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 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
RIcorrect 10.95 0.547 13.79
* 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/TargetSearch.Rcheck/00check.log’
for details.
TargetSearch.Rcheck/00install.out:
* installing *source* package ‘TargetSearch’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Rinit.c -o Rinit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c file.c -o file.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c find_peaks.c -o find_peaks.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c getLine.c -o getLine.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c hpf.c -o hpf.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c ncdf.c -o ncdf.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c netcdf_peak_finding.c -o netcdf_peak_finding.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c peakExtraction.c -o peakExtraction.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c ppc.c -o ppc.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 TargetSearch.so Rinit.o file.o find_peaks.o getLine.o hpf.o ncdf.o netcdf_peak_finding.o peakExtraction.o ppc.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/TargetSearch.Rcheck/TargetSearch/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TargetSearch)
TargetSearch.Rcheck/TargetSearch-Ex.timings:
name | user | system | elapsed
|
FAMEoutliers | 0.112 | 0.013 | 0.127 |
|
FindPeaks | 0.521 | 0.019 | 0.548 |
|
ImportFameSettings | 0.010 | 0.001 | 0.012 |
|
ImportLibrary | 0.019 | 0.001 | 0.021 |
|
ImportSamples | 0.004 | 0.001 | 0.005 |
|
NetCDFPeakFinding | 1.256 | 0.083 | 1.523 |
|
Profile | 2.368 | 0.097 | 3.385 |
|
ProfileCleanUp | 2.189 | 0.074 | 3.344 |
|
RIcorrect | 10.950 | 0.547 | 13.790 |
|
fixRI | 1.210 | 0.063 | 1.741 |
|
medianRILib | 1.058 | 0.028 | 1.307 |
|
peakFind | 0.554 | 0.015 | 0.679 |
|
plotFAME | 0.016 | 0.002 | 0.028 |
|
plotPeak | 0.301 | 0.021 | 0.385 |
|
plotPeakSimple | 0.481 | 0.039 | 0.701 |
|
plotRIdev | 0.806 | 0.035 | 1.280 |
|
plotSpectra | 0.566 | 0.017 | 0.706 |
|
quantMatrix | 1.886 | 0.063 | 2.761 |
|
ri2rt | 0.007 | 0.001 | 0.015 |
|
riMatrix | 0.809 | 0.051 | 0.981 |
|
rt2ri | 0.007 | 0.001 | 0.014 |
|
sampleRI | 1.122 | 0.032 | 1.450 |
|
tsLib-class | 0.008 | 0.001 | 0.019 |
|
tsMSdata-class | 0.001 | 0.001 | 0.003 |
|
tsProfile-class | 0.001 | 0.000 | 0.003 |
|
tsRim-class | 0.003 | 0.000 | 0.005 |
|
tsSample-class | 0.053 | 0.004 | 0.127 |
|
writeLibText | 0.044 | 0.003 | 0.099 |
|