Back to Multiple platform build/check report for BioC 3.14
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-07-30 12:04:35 -0400 (Fri, 30 Jul 2021).

CHECK results for flagme on nebbiolo2

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
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 627/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flagme 1.49.0  (landing page)
Mark Robinson , Riccardo Romoli
Snapshot Date: 2021-07-29 14:50:07 -0400 (Thu, 29 Jul 2021)
URL: https://git.bioconductor.org/packages/flagme
Branch: master
Last Commit: 214f9ee
Last Changed Date: 2021-05-19 11:42:23 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  NO, package depends on 'xcms' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: flagme
Version: 1.49.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings flagme_1.49.0.tar.gz
StartedAt: 2021-07-29 19:44:30 -0400 (Thu, 29 Jul 2021)
EndedAt: 2021-07-29 19:52:16 -0400 (Thu, 29 Jul 2021)
EllapsedTime: 465.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flagme.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings flagme_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/flagme.Rcheck’
* using R version 4.1.0 beta (2021-05-03 r80259)
* 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 ‘1.49.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: multiple methods tables found for ‘bin’
See ‘/home/biocbuild/bbs-3.14-bioc/meat/flagme.Rcheck/00install.out’ for details.
* 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  36.271  0.300  36.573
plotSpectra          26.227  0.188  26.417
corPrt               24.576  0.125  24.703
ndpRT                24.334  0.172  24.506
dynRT                23.928  0.180  24.109
peaksAlignment       23.516  0.304  23.821
retFatMatrix         16.044  0.056  16.100
addXCMSPeaks          9.421  0.058   9.474
imputePeaks           7.296  0.016   7.312
plot                  6.190  0.024   6.215
rmaFitUnit            5.978  0.024   6.001
progressiveAlignment  5.569  0.020   5.589
gatherInfo            5.403  0.028   5.431
calcTimeDiffs         5.345  0.048   5.393
dp                    5.142  0.040   5.182
multipleAlignment     5.123  0.004   5.126
* 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 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/flagme.Rcheck/00check.log’
for details.



Installation output

flagme.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL flagme
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘flagme’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c pearson.c -o pearson.o
gcc -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-flagme/00new/flagme/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
multiple methods tables found for ‘bin’ 
** 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: multiple methods tables found for ‘bin’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for ‘bin’
** testing if installed package keeps a record of temporary installation path
* DONE (flagme)

Tests output


Example timings

flagme.Rcheck/flagme-Ex.timings

nameusersystemelapsed
addAMDISPeaks4.2640.1204.384
addChromaTOFPeaks2.7370.0482.786
addXCMSPeaks9.4210.0589.474
betweenAlignment000
calcTimeDiffs5.3450.0485.393
clusterAlignment4.3760.0604.435
compress4.5390.0714.609
corPrt24.576 0.12524.703
dp5.1420.0405.182
dynRT23.928 0.18024.109
gatherInfo5.4030.0285.431
imputePeaks7.2960.0167.312
multipleAlignment5.1230.0045.126
ndpRT24.334 0.17224.506
normDotProduct4.5570.0244.580
parseChromaTOF2.1350.0042.139
parseELU1.7200.0001.719
peaksAlignment23.516 0.30423.821
peaksDataset4.0320.0204.052
plot6.1900.0246.215
plotImage2.7840.0122.797
plotMultipleSpectra36.271 0.30036.573
plotSpectra26.227 0.18826.417
progressiveAlignment5.5690.0205.589
retFatMatrix16.044 0.05616.100
rmaFitUnit5.9780.0246.001