Back to the "Multiple platform build/check report" A  B  C  D  E [F] G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.5: CHECK report for flagme on veracruz2

This page was generated on 2017-08-16 13:28:26 -0400 (Wed, 16 Aug 2017).

Package 443/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flagme 1.32.0
Mark Robinson , Riccardo Romoli
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/flagme
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 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
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: flagme
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flagme_1.32.0.tar.gz
StartedAt: 2017-08-16 02:43:29 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 02:51:16 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 466.4 seconds
RetCode: 0
Status:  OK 
CheckDir: flagme.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flagme_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/flagme.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 ‘flagme/DESCRIPTION’ ... OK
* this is package ‘flagme’ version ‘1.32.0’
* 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 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 ... OK
* 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
retFatMatrix         27.662  0.739  28.937
ndpRT                26.340  0.593  27.609
dynRT                25.544  0.613  26.877
corPrt               25.424  0.618  26.615
peaksAlignment       24.424  0.655  25.840
plotSpectra          23.961  0.603  25.148
imputePeaks          10.692  0.221  11.193
plot                  8.983  0.221   9.486
rmaFitUnit            7.857  0.301   9.095
addXCMSPeaks          7.339  0.181   7.704
progressiveAlignment  7.237  0.196   7.556
calcTimeDiffs         6.775  0.333   7.324
multipleAlignment     6.964  0.120   7.247
addAMDISPeaks         6.678  0.190   7.067
gatherInfo            6.591  0.160   6.968
compress              6.304  0.144   6.523
clusterAlignment      5.973  0.182   6.303
normDotProduct        5.740  0.146   6.043
dp                    5.550  0.138   5.821
peaksDataset          5.052  0.152   5.346
* 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/flagme.Rcheck/00check.log’
for details.


flagme.Rcheck/00install.out:

* installing *source* package ‘flagme’ ...
** 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 /Users/biocbuild/bbs-3.5-bioc/meat/flagme.Rcheck/flagme/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 (flagme)

flagme.Rcheck/flagme-Ex.timings:

nameusersystemelapsed
addAMDISPeaks6.6780.1907.067
addChromaTOFPeaks4.0090.1354.273
addXCMSPeaks7.3390.1817.704
betweenAlignment0.0010.0000.001
calcTimeDiffs6.7750.3337.324
clusterAlignment5.9730.1826.303
compress6.3040.1446.523
corPrt25.424 0.61826.615
dp5.5500.1385.821
dynRT25.544 0.61326.877
gatherInfo6.5910.1606.968
imputePeaks10.692 0.22111.193
multipleAlignment6.9640.1207.247
ndpRT26.340 0.59327.609
normDotProduct5.7400.1466.043
parseChromaTOF3.7730.0083.877
parseELU2.7420.0082.824
peaksAlignment24.424 0.65525.840
peaksDataset5.0520.1525.346
plot8.9830.2219.486
plotImage3.1440.0993.349
plotSpectra23.961 0.60325.148
progressiveAlignment7.2370.1967.556
retFatMatrix27.662 0.73928.937
rmaFitUnit7.8570.3019.095