Back to Multiple platform build/check report for BioC 3.12
ABCDEFGHIJK[L]MNOPQRSTUVWXYZ

CHECK report for logitT on malbec1

This page was generated on 2021-05-06 12:28:06 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the logitT package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 968/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
logitT 1.48.0  (landing page)
Tobias Guennel
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/logitT
Branch: RELEASE_3_12
Last Commit: 2781658
Last Changed Date: 2020-10-27 10:34:15 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: logitT
Version: 1.48.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:logitT.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings logitT_1.48.0.tar.gz
StartedAt: 2021-05-06 02:58:30 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 02:59:08 -0400 (Thu, 06 May 2021)
EllapsedTime: 37.8 seconds
RetCode: 0
Status:   OK  
CheckDir: logitT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:logitT.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings logitT_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/logitT.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘logitT/DESCRIPTION’ ... OK
* this is package ‘logitT’ version ‘1.48.0’
* 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 ‘logitT’ 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 ... NOTE
'library' or 'require' call to ‘affy’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘affy’
  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
logitTAffy: no visible global function definition for ‘featureNames’
logitTAffy: no visible global function definition for ‘pm’
logitTAffy: no visible global function definition for ‘mm’
logitTAffy: no visible global function definition for ‘pmindex’
Undefined global functions or variables:
  featureNames mm pm pmindex
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.12-bioc/R/library/logitT/libs/logitT.so’:
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
logitTAffy 7.148  0.156   7.555
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/logitT.Rcheck/00check.log’
for details.



Installation output

logitT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL logitT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘logitT’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c logitTfunc.c -o logitTfunc.o
gcc -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o logitT.so logitTfunc.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-logitT/00new/logitT/libs
** R
** 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 (logitT)

Tests output


Example timings

logitT.Rcheck/logitT-Ex.timings

nameusersystemelapsed
logitTAffy7.1480.1567.555