Back to Multiple platform build/check report for BioC 3.11
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

CHECK report for ISoLDE on machv2

This page was generated on 2020-10-17 11:58:45 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ISoLDE PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 903/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ISoLDE 1.16.0
Christelle Reynès
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/ISoLDE
Branch: RELEASE_3_11
Last Commit: 6a71aea
Last Changed Date: 2020-04-27 14:55:49 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ ERROR ] OK 

Summary

Package: ISoLDE
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ISoLDE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ISoLDE_1.16.0.tar.gz
StartedAt: 2020-10-17 02:20:24 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:21:04 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 39.8 seconds
RetCode: 1
Status:  ERROR 
CheckDir: ISoLDE.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ISoLDE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ISoLDE_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ISoLDE.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ISoLDE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ISoLDE’ version ‘1.16.0’
* package encoding: UTF-8
* 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 ‘ISoLDE’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 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 files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘ISoLDE_result_on_example.pdf’, ‘vignette.Rnw’, ‘workflow.pdf’
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/vignette.Rnw’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testsIsolde.R’
 ERROR
Running the tests in ‘tests/testsIsolde.R’ failed.
Last 13 lines of output:
  Done
  > normASRcounts <- readNormInput(norm_file = normfile, del = "tab", rownames = TRUE, colnames = TRUE, dec = ".")
  Reading normalized input file...
  Done
  > target <- readTarget(target_file = targetfile, asr_counts = rawASRcounts, del = "tab")
  Reading target file...
  Done
  > 
  > res_filterT <- filterT(rawASRcounts = rawASRcounts, normASRcounts = normASRcounts, target = target, bias="parental")
  Filtering your data...
  Error in getStrainValues(target) : 
    ERROR: strain column must contain 2 (and only 2) different values. 
  Values found: 
  Calls: filterT -> getStrainValues
  Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/ISoLDE.Rcheck/00check.log’
for details.


Installation output

ISoLDE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ISoLDE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘ISoLDE’ ...
** 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 Isolde.c -o Isolde.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 ISoLDE.so Isolde.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-ISoLDE/00new/ISoLDE/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 (ISoLDE)

Tests output

ISoLDE.Rcheck/tests/testsIsolde.Rout.fail


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ISoLDE)
> 
> targetfile <- system.file("extdata", "target_file.txt", package = "ISoLDE")
> rawfile <- system.file("extdata", "rawASRcounts_file.txt", package = "ISoLDE")
> normfile <- system.file("extdata", "normASRcounts_file.txt", package = "ISoLDE")
> 
> rawASRcounts <- readRawInput(raw_file = rawfile, del = "tab", rownames = TRUE, colnames = TRUE)
Reading raw input file...
Done
> normASRcounts <- readNormInput(norm_file = normfile, del = "tab", rownames = TRUE, colnames = TRUE, dec = ".")
Reading normalized input file...
Done
> target <- readTarget(target_file = targetfile, asr_counts = rawASRcounts, del = "tab")
Reading target file...
Done
> 
> res_filterT <- filterT(rawASRcounts = rawASRcounts, normASRcounts = normASRcounts, target = target, bias="parental")
Filtering your data...
Error in getStrainValues(target) : 
  ERROR: strain column must contain 2 (and only 2) different values. 
Values found: 
Calls: filterT -> getStrainValues
Execution halted

Example timings

ISoLDE.Rcheck/ISoLDE-Ex.timings

nameusersystemelapsed
filterT0.7730.0230.796
filteredASRcounts0.0300.0020.033
isolde_test2.9950.0643.065
normASRcounts0.6090.0220.632
rawASRcounts0.1860.0060.192
readNormInput0.5380.0070.546
readRawInput0.1650.0050.170
readTarget0.0840.0030.088