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CHECK report for flagme on malbec1

This page was generated on 2020-04-15 12:05:25 -0400 (Wed, 15 Apr 2020).

Package 576/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flagme 1.42.0
Mark Robinson , Riccardo Romoli
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/flagme
Branch: RELEASE_3_10
Last Commit: 946e020
Last Changed Date: 2019-10-29 13:08:01 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: flagme
Version: 1.42.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings flagme_1.42.0.tar.gz
StartedAt: 2020-04-15 00:34:57 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:43:47 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 529.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flagme.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings flagme_1.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/flagme.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.42.0’
* 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  45.740  0.212  46.081
corPrt               34.320  0.380  34.832
dynRT                34.216  0.168  34.536
ndpRT                33.316  0.140  33.526
peaksAlignment       32.804  0.208  33.079
plotSpectra          31.640  0.088  31.823
retFatMatrix         19.176  0.072  19.298
imputePeaks          10.952  0.068  11.085
addXCMSPeaks          9.532  0.448  10.034
plot                  8.492  0.012   8.523
multipleAlignment     8.064  0.008   8.100
rmaFitUnit            6.968  0.004   6.986
dp                    6.644  0.044   6.711
calcTimeDiffs         6.608  0.052   6.751
gatherInfo            6.644  0.012   6.674
progressiveAlignment  6.176  0.008   6.190
addAMDISPeaks         5.976  0.132   6.274
compress              6.032  0.056   6.098
peaksDataset          5.848  0.024   5.895
clusterAlignment      5.684  0.032   5.734
normDotProduct        5.668  0.020   5.700
* 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-3.10-bioc/meat/flagme.Rcheck/00check.log’
for details.



Installation output

flagme.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL flagme
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘flagme’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c pearson.c -o pearson.o
gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-flagme/00new/flagme/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
replacing previous import ‘xcms::plot’ by ‘graphics::plot’ when loading ‘CAMERA’ 
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘flagme.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘xcms::plot’ by ‘graphics::plot’ when loading ‘CAMERA’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘xcms::plot’ by ‘graphics::plot’ when loading ‘CAMERA’
** testing if installed package keeps a record of temporary installation path
* DONE (flagme)

Tests output


Example timings

flagme.Rcheck/flagme-Ex.timings

nameusersystemelapsed
addAMDISPeaks5.9760.1326.274
addChromaTOFPeaks4.9760.0164.998
addXCMSPeaks 9.532 0.44810.034
betweenAlignment0.0000.0000.001
calcTimeDiffs6.6080.0526.751
clusterAlignment5.6840.0325.734
compress6.0320.0566.098
corPrt34.320 0.38034.832
dp6.6440.0446.711
dynRT34.216 0.16834.536
gatherInfo6.6440.0126.674
imputePeaks10.952 0.06811.085
multipleAlignment8.0640.0088.100
ndpRT33.316 0.14033.526
normDotProduct5.6680.0205.700
parseChromaTOF3.5560.0003.645
parseELU3.0000.0043.012
peaksAlignment32.804 0.20833.079
peaksDataset5.8480.0245.895
plot8.4920.0128.523
plotImage3.7840.0163.817
plotMultipleSpectra45.740 0.21246.081
plotSpectra31.640 0.08831.823
progressiveAlignment6.1760.0086.190
retFatMatrix19.176 0.07219.298
rmaFitUnit6.9680.0046.986