Mark Robinson
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/flagme |
| Branch: RELEASE_3_7 |
| Last Commit: 87b2065 |
| Last Changed Date: 2018-04-30 10:35:10 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:47:59 -0400 (Wed, 17 Oct 2018).
| Package 492/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flagme 1.36.0 Mark Robinson
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: flagme |
| Version: 1.36.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flagme_1.36.0.tar.gz |
| StartedAt: 2018-10-16 21:21:42 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 21:30:53 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 550.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flagme.Rcheck |
| Warnings: 2 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flagme.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flagme_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/flagme.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flagme/DESCRIPTION’ ... OK
* this is package ‘flagme’ version ‘1.36.0’
* 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
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 or elapsed time > 5s
user system elapsed
plotMultipleSpectra 48.823 2.240 51.430
plotSpectra 35.166 1.675 37.113
peaksAlignment 34.363 1.504 36.076
ndpRT 33.343 1.454 34.950
dynRT 31.233 1.610 32.980
corPrt 30.697 1.588 32.340
retFatMatrix 20.045 0.674 20.872
imputePeaks 11.579 0.322 11.976
plot 10.212 0.340 10.630
addXCMSPeaks 10.100 0.319 10.458
rmaFitUnit 8.059 0.505 8.615
calcTimeDiffs 7.135 0.535 7.686
progressiveAlignment 7.398 0.245 7.683
multipleAlignment 7.157 0.176 7.384
compress 6.668 0.190 6.882
gatherInfo 6.526 0.295 6.856
normDotProduct 6.354 0.232 6.610
clusterAlignment 6.156 0.307 6.487
peaksDataset 6.144 0.238 6.425
dp 6.023 0.260 6.300
addAMDISPeaks 4.861 0.294 5.179
* 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
‘/Users/biocbuild/bbs-3.7-bioc/meat/flagme.Rcheck/00check.log’
for details.
flagme.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flagme ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘flagme’ ... ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c dp.c -o dp.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c pearson.c -o pearson.o clang -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/3.5/Resources/library/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 * DONE (flagme)
flagme.Rcheck/flagme-Ex.timings
| name | user | system | elapsed | |
| addAMDISPeaks | 4.861 | 0.294 | 5.179 | |
| addChromaTOFPeaks | 4.114 | 0.123 | 4.248 | |
| addXCMSPeaks | 10.100 | 0.319 | 10.458 | |
| betweenAlignment | 0.001 | 0.000 | 0.001 | |
| calcTimeDiffs | 7.135 | 0.535 | 7.686 | |
| clusterAlignment | 6.156 | 0.307 | 6.487 | |
| compress | 6.668 | 0.190 | 6.882 | |
| corPrt | 30.697 | 1.588 | 32.340 | |
| dp | 6.023 | 0.260 | 6.300 | |
| dynRT | 31.233 | 1.610 | 32.980 | |
| gatherInfo | 6.526 | 0.295 | 6.856 | |
| imputePeaks | 11.579 | 0.322 | 11.976 | |
| multipleAlignment | 7.157 | 0.176 | 7.384 | |
| ndpRT | 33.343 | 1.454 | 34.950 | |
| normDotProduct | 6.354 | 0.232 | 6.610 | |
| parseChromaTOF | 3.943 | 0.017 | 3.988 | |
| parseELU | 3.265 | 0.010 | 3.295 | |
| peaksAlignment | 34.363 | 1.504 | 36.076 | |
| peaksDataset | 6.144 | 0.238 | 6.425 | |
| plot | 10.212 | 0.340 | 10.630 | |
| plotImage | 3.896 | 0.197 | 4.111 | |
| plotMultipleSpectra | 48.823 | 2.240 | 51.430 | |
| plotSpectra | 35.166 | 1.675 | 37.113 | |
| progressiveAlignment | 7.398 | 0.245 | 7.683 | |
| retFatMatrix | 20.045 | 0.674 | 20.872 | |
| rmaFitUnit | 8.059 | 0.505 | 8.615 | |