Package: ISoLDE

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ISoLDE_1.6.0.tar.gz

StartedAt: 2018-04-12 05:25:08 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 05:26:49 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 100.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ISoLDE.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ISoLDE_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ISoLDE.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.6.0’
* 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 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 ... 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 compiled code ... OK
* 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’
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testsIsolde.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/ISoLDE.Rcheck/00check.log’
for details.

* installing *source* package ‘ISoLDE’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c Isolde.c -o Isolde.o
clang++ -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 -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/ISoLDE.Rcheck/ISoLDE/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ISoLDE)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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...
Filtering threshold is 3
Done
> filteredASRcounts <- res_filterT$filteredASRcounts
> resiso<-isolde_test(bias = "parental", asr_counts = filteredASRcounts, target = target, graph = TRUE, text = FALSE, ext = "png", nboot = 3000,pcore=1)
Warning: pcore is a percentage between 0 and 100, be sure you want to use 1% of your available cores.
ISoLDE is searching for allele-specific gene expression due to parental biases...
Done
According to the satisfying number of replicates the full method can be applied. See the vignette for more details
Testing...
This step can last for a few minutes. Please be patient :)
Note: the full method uses a bootstrap step which means some results might change from one test to another.
Open MP enabled 
Have Cores : 8 
UseCores : 1 
nu0= 0.200000 
Open MP enabled 
Have Cores : 8 
UseCores : 1 
lambda0 : 1.600000 
Open MP enabled 
Have Cores : 8 
UseCores : 1 
nu0= 0.100000 
Open MP enabled 
Have Cores : 8 
UseCores : 1 
lambda0 : 1.500000 
Open MP enabled 
Have Cores : 8 
UseCores : 1 
nu0= 0.200000 
Open MP enabled 
Have Cores : 8 
UseCores : 1 
lambda0 : 1.600000 
Done
52 allele specific expressed (ASE) genes found and written in file ISoLDE_result_ASE_04-12-2018_05-26-39.tsv.
6068 biallelic (BA) genes found and written in file ISoLDE_result_BA_04-12-2018_05-26-39.tsv.
57 Undetermined (UN) genes found and written in file ISoLDE_result_UN_04-12-2018_05-26-39.tsv.
Among these undetermined (UN) genes, 24 genes are coherent.
These genes correspond to the ones with the flag column set on "FLAG_consistency" of "FLAG_significance" in the undetermined genes file. See the vignette for more information on flags.
0 genes have been filtered due to few reads.
> res_filterT <- filterT(rawASRcounts = rawASRcounts, normASRcounts = normASRcounts, target = target, bias="strain")
Filtering your data...
Filtering threshold is 3
Done
> filteredASRcounts <- res_filterT$filteredASRcounts
> resiso<-isolde_test(bias = "strain", asr_counts = filteredASRcounts, target = target, graph = TRUE, text = FALSE, ext = "png", nboot = 3000, method = "threshold")
ISoLDE is searching for allele-specific gene expression due to strain biases...
The predefined threshold method is about to proceed, but we strongly recommand the bootstrap method because ISoLDE detected more than 2 replicates in each cross.
Testing...
Done
308 allele specific expressed (ASE) genes found and written in file ISoLDE_result_ASE_04-12-2018_05-26-41.tsv.
4622 biallelic (BA) genes found and written in file ISoLDE_result_BA_04-12-2018_05-26-41.tsv.
1330 Undetermined (UN) genes found and written in file ISoLDE_result_UN_04-12-2018_05-26-41.tsv.
Among these undetermined (UN) genes, 913 genes are coherent.
These genes correspond to the ones with the flag column set on "FLAG_consistency" of "FLAG_significance" in the undetermined genes file. See the vignette for more information on flags.
0 genes have been filtered due to few reads.
> 
> proc.time()
   user  system elapsed 
 66.852   0.856  68.790 

name	user	system	elapsed
filterT	0.577	0.021	0.600
filteredASRcounts	0.019	0.003	0.023
isolde_test	2.065	0.044	2.126
normASRcounts	0.522	0.007	0.536
rawASRcounts	0.171	0.004	0.177
readNormInput	0.616	0.005	0.627
readRawInput	0.191	0.006	0.199
readTarget	0.077	0.003	0.080