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BioC 3.4: CHECK report for flagme on zin1

This page was generated on 2016-09-21 03:36:41 -0700 (Wed, 21 Sep 2016).

Package 406/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flagme 1.29.0
Mark Robinson , Riccardo Romoli
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flagme
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flagme
Version: 1.29.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings flagme_1.29.0.tar.gz
StartedAt: 2016-09-20 06:21:54 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 06:24:27 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 153.1 seconds
RetCode: 0
Status:  OK 
CheckDir: flagme.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings flagme_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/flagme.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flagme/DESCRIPTION’ ... OK
* this is package ‘flagme’ version ‘1.29.0’
* 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 ... NOTE
.corP: no visible global function definition for ‘complete.cases’
addXCMSPeaks : <anonymous> : <anonymous>: no visible global function
  definition for ‘aggregate’
rmaFitUnit: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  aggregate complete.cases model.matrix
Consider adding
  importFrom("stats", "aggregate", "complete.cases", "model.matrix")
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
imputePeaks 5.220  0.008   5.255
plotSpectra 5.168  0.056   5.223
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/flagme.Rcheck/00check.log’
for details.


flagme.Rcheck/00install.out:

* installing *source* package ‘flagme’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c dp.c -o dp.o
dp.c: In function ‘dp’:
dp.c:263:26: warning: ‘cur_min’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    D[(i+1)+(j+1)*(nr+1)] = cur_min;
                          ^
dp.c:264:28: warning: ‘tb’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    phi[(i+1)+(j+1)*(nr+1)] = tb;
                            ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c pearson.c -o pearson.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/flagme.Rcheck/flagme/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘flagme’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flagme)

flagme.Rcheck/flagme-Ex.timings:

nameusersystemelapsed
addAMDISPeaks2.9200.0603.025
addChromaTOFPeaks1.8720.0121.884
addXCMSPeaks2.3960.0082.407
betweenAlignment0.0000.0000.001
calcTimeDiffs2.7320.0082.767
clusterAlignment2.5760.0122.589
compress2.5840.0162.600
correlationAlignment-class0.0000.0000.001
correlationAlignment3.1200.0443.163
dp2.5040.0162.519
gatherInfo2.8000.0202.817
imputePeaks5.2200.0085.255
multipleAlignment2.9120.0082.919
normDotProduct2.7320.0082.740
parseChromaTOF3.1200.0003.127
parseELU2.3160.0002.316
peaksAlignment0.0040.0000.000
peaksDataset2.7280.0002.747
plot3.9360.0003.933
plotImage1.6520.0241.676
plotSpectra5.1680.0565.223
progressiveAlignment2.8920.0242.918
retFatMatrix3.0720.0083.078
rmaFitUnit2.5200.0162.533