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This page was generated on 2022-01-07 11:07:53 -0500 (Fri, 07 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4077
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4051
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2021-11-01 r81125) -- "Unsuffered Consequences" 4069
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for inveRsion on merida1


To the developers/maintainers of the inveRsion package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/inveRsion.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 946/2073HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
inveRsion 1.43.0  (landing page)
Alejandro Caceres
Snapshot Date: 2022-01-06 13:55:12 -0500 (Thu, 06 Jan 2022)
git_url: https://git.bioconductor.org/packages/inveRsion
git_branch: master
git_last_commit: fba727a
git_last_commit_date: 2021-10-26 11:58:20 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: inveRsion
Version: 1.43.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:inveRsion.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings inveRsion_1.43.0.tar.gz
StartedAt: 2022-01-07 02:43:43 -0500 (Fri, 07 Jan 2022)
EndedAt: 2022-01-07 02:46:19 -0500 (Fri, 07 Jan 2022)
EllapsedTime: 156.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: inveRsion.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:inveRsion.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings inveRsion_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/inveRsion.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.43.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘inveRsion’ can be installed ... OK
* 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 ... WARNING
Undocumented S4 methods:
  generic 'plot' and siglist 'GenoDat,ANY'
  generic 'plot' and siglist 'accuracy,ANY'
  generic 'plot' and siglist 'inversionList,ANY'
  generic 'plot' and siglist 'scan,ANY'
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 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* 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, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/inveRsion.Rcheck/00check.log’
for details.



Installation output

inveRsion.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL inveRsion
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘inveRsion’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init_inveRsion.c -o init_inveRsion.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c inversionModel.c -o inversionModel.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c writeGenoDat.c -o writeGenoDat.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o inveRsion.so init_inveRsion.o inversionModel.o writeGenoDat.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/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-class0.0070.0030.010
GenoDatROI-class0.0200.0040.025
HaploCode-class0.0970.0120.108
ac0.0030.0020.005
accBic1.8110.0591.873
accuracy-class0.0280.0020.031
codeHaplo0.0830.0030.086
gDat0.0060.0020.007
getClassif-methods0.2350.0030.238
getInv-methods0.0020.0020.005
getROIs-methods0.0030.0020.004
hapCode0.0160.0030.019
invList0.0040.0020.006
inveRsion-package0.0010.0000.000
inversionList-class0.0050.0020.006
listInv-methods0.5510.0100.563
scan-class0.0130.0020.016
scanInv0.0710.0040.075
scanRes0.0070.0020.008
setUpGenoDatFile0.0110.0020.013