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This page was generated on 2021-07-30 12:05:28 -0400 (Fri, 30 Jul 2021).

CHECK results for flagme on merida1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flagme_1.49.0.tar.gz
StartedAt: 2021-07-30 02:27:47 -0400 (Fri, 30 Jul 2021)
EndedAt: 2021-07-30 02:39:27 -0400 (Fri, 30 Jul 2021)
EllapsedTime: 700.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flagme.Rcheck
Warnings: 3

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flagme_1.49.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/flagme.Rcheck’
* using R version 4.1.0 RC (2021-05-16 r80304)
* using platform: x86_64-apple-darwin17.0 (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 ‘/Users/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 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 (user + system) or elapsed time > 5s
                       user system elapsed
plotMultipleSpectra  52.936  1.270  54.518
peaksAlignment       37.756  0.907  38.730
ndpRT                37.658  0.815  38.535
corPrt               37.312  0.798  38.166
dynRT                37.226  0.877  38.162
plotSpectra          35.994  0.859  36.915
retFatMatrix         21.305  0.359  21.701
addXCMSPeaks         13.388  0.240  13.642
imputePeaks          12.376  0.204  12.600
plot                  9.960  0.189  10.163
calcTimeDiffs         8.785  0.284   9.121
rmaFitUnit            8.655  0.282   8.957
gatherInfo            8.295  0.167   8.473
multipleAlignment     8.312  0.118   8.439
progressiveAlignment  7.983  0.184   8.179
normDotProduct        7.229  0.156   7.397
dp                    6.895  0.149   7.055
peaksDataset          6.804  0.147   6.964
clusterAlignment      6.449  0.127   6.593
addAMDISPeaks         6.218  0.250   6.478
compress              5.773  0.174   5.951
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/flagme.Rcheck/00check.log’
for details.



Installation output

flagme.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flagme
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘flagme’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c dp.c -o dp.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pearson.c -o pearson.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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
addAMDISPeaks6.2180.2506.478
addChromaTOFPeaks4.4200.1194.542
addXCMSPeaks13.388 0.24013.642
betweenAlignment0.0000.0000.001
calcTimeDiffs8.7850.2849.121
clusterAlignment6.4490.1276.593
compress5.7730.1745.951
corPrt37.312 0.79838.166
dp6.8950.1497.055
dynRT37.226 0.87738.162
gatherInfo8.2950.1678.473
imputePeaks12.376 0.20412.600
multipleAlignment8.3120.1188.439
ndpRT37.658 0.81538.535
normDotProduct7.2290.1567.397
parseChromaTOF4.0640.0264.095
parseELU3.6820.0103.699
peaksAlignment37.756 0.90738.730
peaksDataset6.8040.1476.964
plot 9.960 0.18910.163
plotImage4.1950.0844.290
plotMultipleSpectra52.936 1.27054.518
plotSpectra35.994 0.85936.915
progressiveAlignment7.9830.1848.179
retFatMatrix21.305 0.35921.701
rmaFitUnit8.6550.2828.957