Mark Robinson
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/flagme |
| Branch: RELEASE_3_9 |
| Last Commit: 2034f83 |
| Last Changed Date: 2019-05-02 11:53:11 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:47:18 -0400 (Wed, 16 Oct 2019).
| Package 553/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flagme 1.40.0 Mark Robinson
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: flagme |
| Version: 1.40.0 |
| 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_1.40.0.tar.gz |
| StartedAt: 2019-10-16 02:48:12 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:02:19 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 846.5 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_1.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/flagme.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.40.0’
* 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 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 65.285 5.594 70.906
ndpRT 51.502 3.774 55.294
corPrt 51.012 3.420 54.448
plotSpectra 50.208 3.928 54.158
peaksAlignment 50.051 3.914 53.967
dynRT 48.380 3.350 51.739
retFatMatrix 27.956 1.380 29.507
imputePeaks 16.819 0.891 17.714
plot 15.994 0.928 16.922
addXCMSPeaks 15.760 0.884 16.647
calcTimeDiffs 11.757 1.252 13.019
rmaFitUnit 11.806 1.189 13.020
gatherInfo 11.277 0.557 11.841
progressiveAlignment 11.114 0.686 11.802
multipleAlignment 10.641 0.580 11.221
clusterAlignment 10.462 0.570 11.034
normDotProduct 10.052 0.624 10.676
compress 10.012 0.473 10.487
dp 9.900 0.463 10.365
addAMDISPeaks 9.440 0.578 10.026
peaksDataset 9.285 0.541 9.827
addChromaTOFPeaks 7.406 0.416 7.822
plotImage 6.960 0.409 7.371
* 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-3.9-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/3.6/Resources/library’ * installing *source* package ‘flagme’ ... ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c dp.c -o dp.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/3.6/Resources/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)
flagme.Rcheck/flagme-Ex.timings
| name | user | system | elapsed | |
| addAMDISPeaks | 9.440 | 0.578 | 10.026 | |
| addChromaTOFPeaks | 7.406 | 0.416 | 7.822 | |
| addXCMSPeaks | 15.760 | 0.884 | 16.647 | |
| betweenAlignment | 0 | 0 | 0 | |
| calcTimeDiffs | 11.757 | 1.252 | 13.019 | |
| clusterAlignment | 10.462 | 0.570 | 11.034 | |
| compress | 10.012 | 0.473 | 10.487 | |
| corPrt | 51.012 | 3.420 | 54.448 | |
| dp | 9.900 | 0.463 | 10.365 | |
| dynRT | 48.380 | 3.350 | 51.739 | |
| gatherInfo | 11.277 | 0.557 | 11.841 | |
| imputePeaks | 16.819 | 0.891 | 17.714 | |
| multipleAlignment | 10.641 | 0.580 | 11.221 | |
| ndpRT | 51.502 | 3.774 | 55.294 | |
| normDotProduct | 10.052 | 0.624 | 10.676 | |
| parseChromaTOF | 4.577 | 0.029 | 4.608 | |
| parseELU | 3.746 | 0.033 | 3.779 | |
| peaksAlignment | 50.051 | 3.914 | 53.967 | |
| peaksDataset | 9.285 | 0.541 | 9.827 | |
| plot | 15.994 | 0.928 | 16.922 | |
| plotImage | 6.960 | 0.409 | 7.371 | |
| plotMultipleSpectra | 65.285 | 5.594 | 70.906 | |
| plotSpectra | 50.208 | 3.928 | 54.158 | |
| progressiveAlignment | 11.114 | 0.686 | 11.802 | |
| retFatMatrix | 27.956 | 1.380 | 29.507 | |
| rmaFitUnit | 11.806 | 1.189 | 13.020 | |