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CHECK report for flagme on celaya2

This page was generated on 2019-04-09 12:56:25 -0400 (Tue, 09 Apr 2019).

Package 544/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flagme 1.39.1
Mark Robinson , Riccardo Romoli
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/flagme
Branch: master
Last Commit: a58e346
Last Changed Date: 2019-01-04 13:31:24 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: flagme
Version: 1.39.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flagme_1.39.1.tar.gz
StartedAt: 2019-04-09 01:55:37 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:10:07 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 870.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flagme.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flagme_1.39.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/flagme.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flagme/DESCRIPTION’ ... OK
* this is package ‘flagme’ version ‘1.39.1’
* checking package namespace information ... NOTE
  Namespace with empty importFrom: ‘gcspikelite’
* 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 ‘flagme’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking Rd files ... WARNING
man/plotMultipleSpectra.Rd: non-ASCII input and no declared encoding
problem found in ‘plotMultipleSpectra.Rd’
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'show' and siglist 'betweenAlignment'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... NOTE
Note: information on .o files is not available
* 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
plotMultipleSpectra  72.273  5.413  77.702
corPrt               57.385  3.617  61.022
plotSpectra          56.323  3.581  60.029
peaksAlignment       54.764  3.979  58.746
ndpRT                54.361  3.742  58.106
dynRT                54.120  3.903  58.104
retFatMatrix         29.213  1.530  30.744
imputePeaks          19.554  0.870  20.426
addXCMSPeaks         17.326  0.766  18.095
plot                 17.024  1.005  18.032
calcTimeDiffs        13.312  1.155  14.581
rmaFitUnit           13.141  1.288  14.429
multipleAlignment    11.997  0.543  12.540
gatherInfo           11.634  0.627  12.272
dp                   11.241  0.612  11.855
progressiveAlignment 11.293  0.538  11.849
compress             11.174  0.439  11.615
clusterAlignment     10.474  0.488  10.964
peaksDataset         10.056  0.704  10.761
normDotProduct        9.630  0.580  10.209
addAMDISPeaks         8.699  0.586   9.528
addChromaTOFPeaks     7.727  0.426   8.154
plotImage             6.982  0.373   7.356
* 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 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/flagme.Rcheck/00check.log’
for details.



Installation output

flagme.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flagme
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘flagme’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c dp.c -o dp.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c pearson.c -o pearson.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 flagme.so dp.o init.o pearson.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-flagme/00new/flagme/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘flagme.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flagme)

Tests output


Example timings

flagme.Rcheck/flagme-Ex.timings

nameusersystemelapsed
addAMDISPeaks8.6990.5869.528
addChromaTOFPeaks7.7270.4268.154
addXCMSPeaks17.326 0.76618.095
betweenAlignment000
calcTimeDiffs13.312 1.15514.581
clusterAlignment10.474 0.48810.964
compress11.174 0.43911.615
corPrt57.385 3.61761.022
dp11.241 0.61211.855
dynRT54.120 3.90358.104
gatherInfo11.634 0.62712.272
imputePeaks19.554 0.87020.426
multipleAlignment11.997 0.54312.540
ndpRT54.361 3.74258.106
normDotProduct 9.630 0.58010.209
parseChromaTOF4.3730.0434.418
parseELU4.1410.0274.168
peaksAlignment54.764 3.97958.746
peaksDataset10.056 0.70410.761
plot17.024 1.00518.032
plotImage6.9820.3737.356
plotMultipleSpectra72.273 5.41377.702
plotSpectra56.323 3.58160.029
progressiveAlignment11.293 0.53811.849
retFatMatrix29.213 1.53030.744
rmaFitUnit13.141 1.28814.429