- using R version 4.0.2 (2020-06-22)
- using platform: x86_64-apple-darwin17.0 (64-bit)
- using session charset: UTF-8
- checking for file ‘RUVIIIC/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘RUVIIIC’ version ‘1.0.17’
- 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
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- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘RUVIIIC’ can be installed ... [75s/76s] OK
- checking installed package size ... NOTE
installed size is 45.9Mb
sub-directories of 1Mb or more:
libs 45.3Mb
- 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 loading without being on the library search path ... 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 ... [4s/4s] 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
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- 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 ... OK
- checking examples ... [2s/2s] ERROR
Running examples in ‘RUVIIIC-Ex.R’ failed
The error most likely occurred in:
> ### Name: RUVIII_C
> ### Title: RUV-III-C
> ### Aliases: RUVIII_C
>
> ### ** Examples
>
> data(crossLab)
> #Design matrix containing information about which runs are technical replicates of each other.
> #In this case, random pairings of mass-spec runs analysing the same sample, at different sites.
> #Note that we specify no intercept term!
> M <- model.matrix(~ grouping - 1, data = peptideData)
> #Get out the list of peptides, both HEK (control) and peptides of interest.
> peptides <- setdiff(colnames(peptideData), c("filename", "site", "mixture", "Date", "grouping"))
> #Reduce the data matrix to only the peptide data
> onlyPeptideData <- data.matrix(peptideData[, peptides])
> #All the human peptides are potential controls. That is, everything that's not an SIS peptides.
> potentialControls <- setdiff(peptides, sisPeptides)
> #But we want to use controls that are always found
> potentialControlsAlwaysFound <- names(which(apply(onlyPeptideData[, potentialControls], 2,
+ function(x) sum(is.na(x))) == 0))
> #Actually run correction
> #Set number of threads for CRAN
> RUVIIIC::omp_set_num_threads(2L)
Error in RUVIIIC_omp_set_num_threads(num) :
Not built with openmp suppport
Calls: <Anonymous> -> RUVIIIC_omp_set_num_threads
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [5s/5s] OK
Running ‘testthat.R’ [5s/5s]
- checking PDF version of manual ... OK
- DONE
Status: 1 ERROR, 1 NOTE
- using check arguments '--no-clean-on-error '