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CHECK report for CorMut on malbec2

This page was generated on 2020-03-12 13:45:28 -0400 (Thu, 12 Mar 2020).

Package 369/1838HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CorMut 1.29.0
Zhenpeng Li
Snapshot Date: 2020-03-11 16:45:12 -0400 (Wed, 11 Mar 2020)
URL: https://git.bioconductor.org/packages/CorMut
Branch: master
Last Commit: f73865e
Last Changed Date: 2019-10-29 13:36:18 -0400 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CorMut
Version: 1.29.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:CorMut.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings CorMut_1.29.0.tar.gz
StartedAt: 2020-03-12 02:02:15 -0400 (Thu, 12 Mar 2020)
EndedAt: 2020-03-12 02:03:40 -0400 (Thu, 12 Mar 2020)
EllapsedTime: 85.3 seconds
RetCode: 0
Status:  OK 
CheckDir: CorMut.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:CorMut.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings CorMut_1.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/CorMut.Rcheck’
* using R Under development (unstable) (2020-01-28 r77731)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CorMut/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CorMut’ version ‘1.29.0’
* 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 ‘CorMut’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
biCompare-methods 19.294  0.019  19.404
miAA               8.330  0.008   8.339
miCodon            7.267  0.000   7.267
* 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

CorMut.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL CorMut
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘CorMut’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for ‘seq_num.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for ‘kaks.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for ‘lod.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for ‘q.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for ‘ka.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for ‘ks.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for ‘mi.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for ‘p.value.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for ‘ckaks.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for ‘method.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for ‘positiveSite01.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for ‘positiveSite02.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for ‘state_1.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for ‘statistic_1.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for ‘state_2.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
Warning in .recursiveCallTest(body, fname) :
  the body of the generic function for ‘statistic_2.CorMut’ calls 'standardGeneric' to dispatch on a different name ("aslot")!
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CorMut)

Tests output


Example timings

CorMut.Rcheck/CorMut-Ex.timings

nameusersystemelapsed
JI-class000
MI-class0.0010.0000.000
biCkaksCodon-class000
biCompare-class000
biCompare-methods19.294 0.01919.404
ckaks-class000
ckaksAA3.9510.0043.955
ckaksCodon2.2860.0002.287
filterSites-methods1.0190.0001.019
jiAA3.2590.0163.277
kaksAA-class0.0000.0000.001
kaksAA2.0710.0002.071
kaksCodon-class000
kaksCodon2.0290.0002.030
miAA8.3300.0088.339
miCodon7.2670.0007.267
plot-methods4.510.004.51
seqFormat-methods0.7840.0000.784