Mark Robinson
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/flagme |
| Branch: RELEASE_3_10 |
| Last Commit: 946e020 |
| Last Changed Date: 2019-10-29 13:08:01 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:05:25 -0400 (Wed, 15 Apr 2020).
| Package 576/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flagme 1.42.0 Mark Robinson
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: flagme |
| Version: 1.42.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings flagme_1.42.0.tar.gz |
| StartedAt: 2020-04-15 00:34:57 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 00:43:47 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 529.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flagme.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings flagme_1.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/flagme.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.42.0’
* 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 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 45.740 0.212 46.081
corPrt 34.320 0.380 34.832
dynRT 34.216 0.168 34.536
ndpRT 33.316 0.140 33.526
peaksAlignment 32.804 0.208 33.079
plotSpectra 31.640 0.088 31.823
retFatMatrix 19.176 0.072 19.298
imputePeaks 10.952 0.068 11.085
addXCMSPeaks 9.532 0.448 10.034
plot 8.492 0.012 8.523
multipleAlignment 8.064 0.008 8.100
rmaFitUnit 6.968 0.004 6.986
dp 6.644 0.044 6.711
calcTimeDiffs 6.608 0.052 6.751
gatherInfo 6.644 0.012 6.674
progressiveAlignment 6.176 0.008 6.190
addAMDISPeaks 5.976 0.132 6.274
compress 6.032 0.056 6.098
peaksDataset 5.848 0.024 5.895
clusterAlignment 5.684 0.032 5.734
normDotProduct 5.668 0.020 5.700
* 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-3.10-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-3.10-bioc/R/bin/R CMD INSTALL flagme
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘flagme’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pearson.c -o pearson.o
gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-flagme/00new/flagme/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
replacing previous import ‘xcms::plot’ by ‘graphics::plot’ when loading ‘CAMERA’
** 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: replacing previous import ‘xcms::plot’ by ‘graphics::plot’ when loading ‘CAMERA’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘xcms::plot’ by ‘graphics::plot’ when loading ‘CAMERA’
** testing if installed package keeps a record of temporary installation path
* DONE (flagme)
flagme.Rcheck/flagme-Ex.timings
| name | user | system | elapsed | |
| addAMDISPeaks | 5.976 | 0.132 | 6.274 | |
| addChromaTOFPeaks | 4.976 | 0.016 | 4.998 | |
| addXCMSPeaks | 9.532 | 0.448 | 10.034 | |
| betweenAlignment | 0.000 | 0.000 | 0.001 | |
| calcTimeDiffs | 6.608 | 0.052 | 6.751 | |
| clusterAlignment | 5.684 | 0.032 | 5.734 | |
| compress | 6.032 | 0.056 | 6.098 | |
| corPrt | 34.320 | 0.380 | 34.832 | |
| dp | 6.644 | 0.044 | 6.711 | |
| dynRT | 34.216 | 0.168 | 34.536 | |
| gatherInfo | 6.644 | 0.012 | 6.674 | |
| imputePeaks | 10.952 | 0.068 | 11.085 | |
| multipleAlignment | 8.064 | 0.008 | 8.100 | |
| ndpRT | 33.316 | 0.140 | 33.526 | |
| normDotProduct | 5.668 | 0.020 | 5.700 | |
| parseChromaTOF | 3.556 | 0.000 | 3.645 | |
| parseELU | 3.000 | 0.004 | 3.012 | |
| peaksAlignment | 32.804 | 0.208 | 33.079 | |
| peaksDataset | 5.848 | 0.024 | 5.895 | |
| plot | 8.492 | 0.012 | 8.523 | |
| plotImage | 3.784 | 0.016 | 3.817 | |
| plotMultipleSpectra | 45.740 | 0.212 | 46.081 | |
| plotSpectra | 31.640 | 0.088 | 31.823 | |
| progressiveAlignment | 6.176 | 0.008 | 6.190 | |
| retFatMatrix | 19.176 | 0.072 | 19.298 | |
| rmaFitUnit | 6.968 | 0.004 | 6.986 | |