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CHECK report for flagme on malbec2

This page was generated on 2019-10-16 11:57:10 -0400 (Wed, 16 Oct 2019).

Package 553/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flagme 1.40.0
Mark Robinson , Riccardo Romoli
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/flagme
Branch: RELEASE_3_9
Last Commit: 2034f83
Last Changed Date: 2019-05-02 11:53:11 -0400 (Thu, 02 May 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

Summary

Package: flagme
Version: 1.40.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings flagme_1.40.0.tar.gz
StartedAt: 2019-10-16 01:38:31 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:47:01 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 509.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flagme.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings flagme_1.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/flagme.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.40.0’
* 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 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 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  45.427  0.328  45.864
peaksAlignment       34.157  0.360  34.529
corPrt               31.277  0.283  31.774
dynRT                31.200  0.120  31.323
plotSpectra          30.185  0.264  30.449
ndpRT                28.571  0.196  28.768
retFatMatrix         18.015  0.092  18.107
addXCMSPeaks          9.334  0.351   9.706
imputePeaks           9.398  0.020   9.435
plot                  8.328  0.052   8.380
calcTimeDiffs         7.706  0.024   7.885
rmaFitUnit            6.838  0.020   6.859
gatherInfo            6.356  0.036   6.392
progressiveAlignment  6.262  0.020   6.285
dp                    5.988  0.008   5.996
multipleAlignment     5.849  0.004   5.852
clusterAlignment      5.754  0.048   5.802
compress              5.693  0.036   5.729
normDotProduct        5.486  0.024   5.510
peaksDataset          5.324  0.028   5.352
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/flagme.Rcheck/00check.log’
for details.



Installation output

flagme.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL flagme
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘flagme’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c pearson.c -o pearson.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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
addAMDISPeaks4.8270.1004.995
addChromaTOFPeaks3.7870.0323.820
addXCMSPeaks9.3340.3519.706
betweenAlignment0.0000.0000.001
calcTimeDiffs7.7060.0247.885
clusterAlignment5.7540.0485.802
compress5.6930.0365.729
corPrt31.277 0.28331.774
dp5.9880.0085.996
dynRT31.200 0.12031.323
gatherInfo6.3560.0366.392
imputePeaks9.3980.0209.435
multipleAlignment5.8490.0045.852
ndpRT28.571 0.19628.768
normDotProduct5.4860.0245.510
parseChromaTOF2.1390.0002.154
parseELU2.5570.0002.556
peaksAlignment34.157 0.36034.529
peaksDataset5.3240.0285.352
plot8.3280.0528.380
plotImage3.7620.0003.761
plotMultipleSpectra45.427 0.32845.864
plotSpectra30.185 0.26430.449
progressiveAlignment6.2620.0206.285
retFatMatrix18.015 0.09218.107
rmaFitUnit6.8380.0206.859