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This page was generated on 2021-10-15 15:05:44 -0400 (Fri, 15 Oct 2021).

CHECK results for LowMACA on nebbiolo1

To the developers/maintainers of the LowMACA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/LowMACA.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1001/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LowMACA 1.22.0  (landing page)
Stefano de Pretis , Giorgio Melloni
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/LowMACA
git_branch: RELEASE_3_13
git_last_commit: b9b4a18
git_last_commit_date: 2021-05-19 12:12:19 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: LowMACA
Version: 1.22.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:LowMACA.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings LowMACA_1.22.0.tar.gz
StartedAt: 2021-10-14 10:23:56 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:00:42 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 2206.4 seconds
RetCode: 0
Status:   OK  
CheckDir: LowMACA.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:LowMACA.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings LowMACA_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/LowMACA.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LowMACA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LowMACA’ version ‘1.22.0’
* checking package namespace information ... OK
* 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 ‘LowMACA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system  elapsed
allPfamAnalysis   124.569  3.090  127.627
lfmSingleSequence  66.239  1.860   68.096
setup              13.376  0.484 1849.756
LowMACA-class       8.848  0.174   17.840
LowMACA-package     6.374  0.188   11.289
alignSequences      4.731  0.160   20.246
* 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: OK


Installation output

LowMACA.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL LowMACA
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘LowMACA’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Checking if clustalo is in the PATH...
Checking clustalo Version...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
** testing if installed package can be loaded from final location
Checking if clustalo is in the PATH...
Checking clustalo Version...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
** testing if installed package keeps a record of temporary installation path
* DONE (LowMACA)

Tests output


Example timings

LowMACA.Rcheck/LowMACA-Ex.timings

nameusersystemelapsed
BLOSUM620.0090.0000.009
LowMACA-class 8.848 0.17417.840
LowMACA-package 6.374 0.18811.289
LowMACA_AML0.0240.0000.024
alignSequences 4.731 0.16020.246
allPfamAnalysis124.569 3.090127.627
bpAll0.6710.0080.679
entropy0.6520.0040.657
getMutations1.8070.0253.635
lfm1.3530.0261.380
lfmSingleSequence66.239 1.86068.096
lmAlignment0.0390.0080.047
lmEntropy0.6980.0040.701
lmMutations0.0380.0000.038
lmObj0.0760.0080.084
lmParams0.5250.0140.540
lmPlot2.3590.0042.363
lmPlotSingleSequence2.7000.0492.749
mapMutations0.4830.0080.491
newLowMACA2.6120.0602.672
nullProfile0.7090.0120.721
parallelize0.4720.0040.477
protter0.7280.0042.837
setup 13.376 0.4841849.756
showTumorType0.0450.0070.089