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 11:57:10 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings flagme_1.40.0.tar.gz |
| StartedAt: 2019-10-16 01:38:31 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:47:01 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 509.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flagme.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:flagme.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings flagme_1.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/flagme.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.40.0’
* 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 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 45.427 0.328 45.864
peaksAlignment 34.157 0.360 34.529
corPrt 31.277 0.283 31.774
dynRT 31.200 0.120 31.323
plotSpectra 30.185 0.264 30.449
ndpRT 28.571 0.196 28.768
retFatMatrix 18.015 0.092 18.107
addXCMSPeaks 9.334 0.351 9.706
imputePeaks 9.398 0.020 9.435
plot 8.328 0.052 8.380
calcTimeDiffs 7.706 0.024 7.885
rmaFitUnit 6.838 0.020 6.859
gatherInfo 6.356 0.036 6.392
progressiveAlignment 6.262 0.020 6.285
dp 5.988 0.008 5.996
multipleAlignment 5.849 0.004 5.852
clusterAlignment 5.754 0.048 5.802
compress 5.693 0.036 5.729
normDotProduct 5.486 0.024 5.510
peaksDataset 5.324 0.028 5.352
* 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-3.9-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-3.9-bioc/R/bin/R CMD INSTALL flagme
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘flagme’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pearson.c -o pearson.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o flagme.so dp.o init.o pearson.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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 | 4.827 | 0.100 | 4.995 | |
| addChromaTOFPeaks | 3.787 | 0.032 | 3.820 | |
| addXCMSPeaks | 9.334 | 0.351 | 9.706 | |
| betweenAlignment | 0.000 | 0.000 | 0.001 | |
| calcTimeDiffs | 7.706 | 0.024 | 7.885 | |
| clusterAlignment | 5.754 | 0.048 | 5.802 | |
| compress | 5.693 | 0.036 | 5.729 | |
| corPrt | 31.277 | 0.283 | 31.774 | |
| dp | 5.988 | 0.008 | 5.996 | |
| dynRT | 31.200 | 0.120 | 31.323 | |
| gatherInfo | 6.356 | 0.036 | 6.392 | |
| imputePeaks | 9.398 | 0.020 | 9.435 | |
| multipleAlignment | 5.849 | 0.004 | 5.852 | |
| ndpRT | 28.571 | 0.196 | 28.768 | |
| normDotProduct | 5.486 | 0.024 | 5.510 | |
| parseChromaTOF | 2.139 | 0.000 | 2.154 | |
| parseELU | 2.557 | 0.000 | 2.556 | |
| peaksAlignment | 34.157 | 0.360 | 34.529 | |
| peaksDataset | 5.324 | 0.028 | 5.352 | |
| plot | 8.328 | 0.052 | 8.380 | |
| plotImage | 3.762 | 0.000 | 3.761 | |
| plotMultipleSpectra | 45.427 | 0.328 | 45.864 | |
| plotSpectra | 30.185 | 0.264 | 30.449 | |
| progressiveAlignment | 6.262 | 0.020 | 6.285 | |
| retFatMatrix | 18.015 | 0.092 | 18.107 | |
| rmaFitUnit | 6.838 | 0.020 | 6.859 | |