Mark Robinson
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/flagme |
| Branch: RELEASE_3_8 |
| Last Commit: 35fcae3 |
| Last Changed Date: 2019-01-04 13:31:27 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:48:40 -0400 (Tue, 16 Apr 2019).
| Package 521/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flagme 1.38.1 Mark Robinson
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: flagme |
| Version: 1.38.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings flagme_1.38.1.tar.gz |
| StartedAt: 2019-04-15 23:55:14 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-16 00:04:31 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 557.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flagme.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings flagme_1.38.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/flagme.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.38.1’
* 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 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 54.776 0.252 55.187
plotSpectra 38.176 0.196 38.438
peaksAlignment 38.016 0.176 38.247
corPrt 37.160 0.236 37.505
dynRT 36.820 0.124 36.998
ndpRT 35.908 0.116 36.081
retFatMatrix 21.448 0.120 21.600
addXCMSPeaks 11.288 0.344 11.660
imputePeaks 10.380 0.008 10.425
plot 8.668 0.024 8.703
calcTimeDiffs 8.476 0.024 8.579
multipleAlignment 7.492 0.028 7.531
progressiveAlignment 7.404 0.024 7.434
peaksDataset 7.320 0.032 7.361
dp 7.156 0.048 7.209
addAMDISPeaks 6.648 0.104 6.808
clusterAlignment 6.684 0.016 6.726
gatherInfo 6.660 0.012 6.684
compress 6.588 0.032 6.628
rmaFitUnit 6.360 0.020 6.386
normDotProduct 5.580 0.012 5.597
plotImage 4.992 0.024 5.018
* 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-3.8-bioc/meat/flagme.Rcheck/00check.log’
for details.
flagme.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL flagme
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘flagme’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-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]
D[(i+1)+(j+1)*(nr+1)] = cur_min;
^
dp.c:264:28: warning: ‘tb’ may be used uninitialized in this function [-Wmaybe-uninitialized]
phi[(i+1)+(j+1)*(nr+1)] = tb;
^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pearson.c -o pearson.o
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/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 | 6.648 | 0.104 | 6.808 | |
| addChromaTOFPeaks | 4.764 | 0.056 | 4.826 | |
| addXCMSPeaks | 11.288 | 0.344 | 11.660 | |
| betweenAlignment | 0 | 0 | 0 | |
| calcTimeDiffs | 8.476 | 0.024 | 8.579 | |
| clusterAlignment | 6.684 | 0.016 | 6.726 | |
| compress | 6.588 | 0.032 | 6.628 | |
| corPrt | 37.160 | 0.236 | 37.505 | |
| dp | 7.156 | 0.048 | 7.209 | |
| dynRT | 36.820 | 0.124 | 36.998 | |
| gatherInfo | 6.660 | 0.012 | 6.684 | |
| imputePeaks | 10.380 | 0.008 | 10.425 | |
| multipleAlignment | 7.492 | 0.028 | 7.531 | |
| ndpRT | 35.908 | 0.116 | 36.081 | |
| normDotProduct | 5.580 | 0.012 | 5.597 | |
| parseChromaTOF | 4.068 | 0.000 | 4.087 | |
| parseELU | 3.268 | 0.004 | 3.274 | |
| peaksAlignment | 38.016 | 0.176 | 38.247 | |
| peaksDataset | 7.320 | 0.032 | 7.361 | |
| plot | 8.668 | 0.024 | 8.703 | |
| plotImage | 4.992 | 0.024 | 5.018 | |
| plotMultipleSpectra | 54.776 | 0.252 | 55.187 | |
| plotSpectra | 38.176 | 0.196 | 38.438 | |
| progressiveAlignment | 7.404 | 0.024 | 7.434 | |
| retFatMatrix | 21.448 | 0.120 | 21.600 | |
| rmaFitUnit | 6.360 | 0.020 | 6.386 | |