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This page was generated on 2021-08-02 15:04:47 -0400 (Mon, 02 Aug 2021).

CHECK results for flagme on nebbiolo1

To the developers/maintainers of the flagme package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flagme.git to
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raw results

Package 638/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flagme 1.48.0  (landing page)
Mark Robinson , Riccardo Romoli
Snapshot Date: 2021-08-01 04:50:10 -0400 (Sun, 01 Aug 2021)
URL: https://git.bioconductor.org/packages/flagme
Branch: RELEASE_3_13
Last Commit: 31bd595
Last Changed Date: 2021-05-19 11:42:23 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: flagme
Version: 1.48.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings flagme_1.48.0.tar.gz
StartedAt: 2021-08-01 09:47:43 -0400 (Sun, 01 Aug 2021)
EndedAt: 2021-08-01 09:55:36 -0400 (Sun, 01 Aug 2021)
EllapsedTime: 472.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flagme.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings flagme_1.48.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/flagme.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘1.48.0’
* 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 (user + system) or elapsed time > 5s
                       user system elapsed
plotMultipleSpectra  36.546  0.196  36.748
corPrt               26.615  0.257  26.874
plotSpectra          26.220  0.156  26.377
peaksAlignment       25.388  0.220  25.609
dynRT                24.639  0.287  24.936
ndpRT                23.664  0.200  23.865
retFatMatrix         17.700  0.076  17.776
addXCMSPeaks          9.936  0.089  10.023
plot                  6.716  0.020   6.737
imputePeaks           6.702  0.016   6.721
rmaFitUnit            6.213  0.036   6.250
progressiveAlignment  5.512  0.028   5.540
multipleAlignment     5.098  0.024   5.123
calcTimeDiffs         5.069  0.051   5.125
* 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-3.13-bioc/meat/flagme.Rcheck/00check.log’
for details.



Installation output

flagme.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL flagme
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘flagme’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-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]
  263 |    D[(i+1)+(j+1)*(nr+1)] = cur_min;
      |    ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
dp.c:264:28: warning: ‘tb’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  264 |    phi[(i+1)+(j+1)*(nr+1)] = tb;
      |    ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c pearson.c -o pearson.o
gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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
addAMDISPeaks4.5510.1214.676
addChromaTOFPeaks2.7830.0322.816
addXCMSPeaks 9.936 0.08910.023
betweenAlignment000
calcTimeDiffs5.0690.0515.125
clusterAlignment4.3600.0604.421
compress4.4130.0964.509
corPrt26.615 0.25726.874
dp4.9340.0114.946
dynRT24.639 0.28724.936
gatherInfo4.9670.0164.983
imputePeaks6.7020.0166.721
multipleAlignment5.0980.0245.123
ndpRT23.664 0.20023.865
normDotProduct4.6790.0164.695
parseChromaTOF1.9640.0121.979
parseELU1.7710.0121.783
peaksAlignment25.388 0.22025.609
peaksDataset4.4420.0164.458
plot6.7160.0206.737
plotImage2.8270.0202.847
plotMultipleSpectra36.546 0.19636.748
plotSpectra26.220 0.15626.377
progressiveAlignment5.5120.0285.540
retFatMatrix17.700 0.07617.776
rmaFitUnit6.2130.0366.250