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CHECK report for inveRsion on malbec2

This page was generated on 2019-10-16 11:59:35 -0400 (Wed, 16 Oct 2019).

Package 825/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
inveRsion 1.32.0
Alejandro Caceres
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/inveRsion
Branch: RELEASE_3_9
Last Commit: 2bc6b77
Last Changed Date: 2019-05-02 11:53:22 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: inveRsion
Version: 1.32.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:inveRsion.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings inveRsion_1.32.0.tar.gz
StartedAt: 2019-10-16 02:33:59 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:35:16 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 77.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: inveRsion.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:inveRsion.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings inveRsion_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/inveRsion.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 ‘inveRsion/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘inveRsion’ version ‘1.32.0’
* 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 ‘inveRsion’ can be installed ... WARNING
Found the following significant warnings:
  inversionModel.c:185:31: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  inversionModel.c:360:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/biocbuild/bbs-3.9-bioc/meat/inveRsion.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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 ... NOTE
Package in Depends field not imported from: ‘haplo.stats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘inveRsion/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("\n")
    packageStartupMessage("Hola!\n")
    packageStartupMessage("welcome to inevRsion package. \n \n \n")
    packageStartupMessage("type: manual() for full manual \n      vignette(\"inveRsion\") for a quick start \n")

See section ‘Good practice’ in '?.onAttach'.

callEncode: no visible global function definition for ‘quantile’
encodeGeno: no visible global function definition for ‘setupGeno’
encodeGeno: no visible global function definition for ‘haplo.em’
encodeGeno: no visible global function definition for
  ‘haplo.em.control’
encodeGenoAcross: no visible global function definition for ‘setupGeno’
encodeGenoAcross: no visible global function definition for ‘haplo.em’
encodeGenoAcross: no visible global function definition for
  ‘haplo.em.control’
Undefined global functions or variables:
  haplo.em haplo.em.control quantile setupGeno
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/inveRsion.Rcheck/00check.log’
for details.



Installation output

inveRsion.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL inveRsion
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘inveRsion’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c init_inveRsion.c -o init_inveRsion.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c inversionModel.c -o inversionModel.o
inversionModel.c: In function ‘blockAndLev’:
inversionModel.c:185:31: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
         if(dat[(*nr)*(c1)+row]==levelleft[level] & dat[(*nr)*(c2)+row]==levelright[level])
            ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
inversionModel.c: In function ‘inversionModel’:
inversionModel.c:360:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
    while(steps<*maxSteps & tol>mintol)
          ~~~~~^~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c writeGenoDat.c -o writeGenoDat.o
writeGenoDat.c: In function ‘writeGenoDat’:
writeGenoDat.c:103:9: warning: ‘dat’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         fprintf(fg,"%d ", dat-1);
         ^~~~~~~~~~~~~~~~~~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o inveRsion.so init_inveRsion.o inversionModel.o writeGenoDat.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-inveRsion/00new/inveRsion/libs
** 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 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 (inveRsion)

Tests output


Example timings

inveRsion.Rcheck/inveRsion-Ex.timings

nameusersystemelapsed
GenoDat-class0.0030.0000.004
GenoDatROI-class0.010.000.01
HaploCode-class0.0670.0000.067
ac0.0020.0000.002
accBic0.8540.0040.913
accuracy-class0.0170.0040.021
codeHaplo0.0580.0000.058
gDat0.0040.0000.003
getClassif-methods0.0990.0000.099
getInv-methods0.0020.0000.002
getROIs-methods0.0020.0000.002
hapCode0.0080.0000.008
invList0.0030.0000.003
inveRsion-package000
inversionList-class0.0020.0000.002
listInv-methods0.3820.0080.390
scan-class0.0060.0000.006
scanInv0.040.000.04
scanRes0.0040.0000.004
setUpGenoDatFile0.0060.0000.038