Christelle Reynès
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ISoLDE |
| Branch: RELEASE_3_8 |
| Last Commit: a65a412 |
| Last Changed Date: 2019-01-04 13:36:38 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:26:29 -0400 (Sat, 13 Apr 2019).
| Package 801/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ISoLDE 1.10.1 Christelle Reynès
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: ISoLDE |
| Version: 1.10.1 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ISoLDE.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ISoLDE_1.10.1.tar.gz |
| StartedAt: 2019-04-13 03:17:22 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 03:22:44 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 321.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ISoLDE.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ISoLDE.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings ISoLDE_1.10.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/ISoLDE.Rcheck' * using R version 3.5.3 (2019-03-11) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ISoLDE/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ISoLDE' version '1.10.1' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/ISoLDE/libs/i386/ISoLDE.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Found 'printf', possibly from 'printf' (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' ... 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testsIsolde.R' OK ** running tests for arch 'x64' ... Running 'testsIsolde.R' OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/ISoLDE.Rcheck/00check.log' for details.
ISoLDE.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/ISoLDE_1.10.1.tar.gz && rm -rf ISoLDE.buildbin-libdir && mkdir ISoLDE.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ISoLDE.buildbin-libdir ISoLDE_1.10.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL ISoLDE_1.10.1.zip && rm ISoLDE_1.10.1.tar.gz ISoLDE_1.10.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 1258k 100 1258k 0 0 25.2M 0 --:--:-- --:--:-- --:--:-- 27.3M
install for i386
* installing *source* package 'ISoLDE' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O3 -Wall -std=gnu99 -mtune=generic -c Isolde.c -o Isolde.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o ISoLDE.dll tmp.def Isolde.o -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/ISoLDE.buildbin-libdir/ISoLDE/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ISoLDE'
finding HTML links ... done
ISoLDE-package html
filterT html
filteredASRcounts html
isolde_test html
normASRcounts html
rawASRcounts html
readNormInput html
readRawInput html
readTarget html
target html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'ISoLDE' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -fopenmp -O2 -Wall -std=gnu99 -mtune=generic -c Isolde.c -o Isolde.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o ISoLDE.dll tmp.def Isolde.o -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/ISoLDE.buildbin-libdir/ISoLDE/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ISoLDE' as ISoLDE_1.10.1.zip
* DONE (ISoLDE)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'ISoLDE' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
ISoLDE.Rcheck/tests_i386/testsIsolde.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 : 20
UseCores : 1
nu0= 0.100000
Open MP enabled
Have Cores : 20
UseCores : 1
lambda0 : 1.600000
Open MP enabled
Have Cores : 20
UseCores : 1
nu0= 0.100000
Open MP enabled
Have Cores : 20
UseCores : 1
lambda0 : 1.600000
Open MP enabled
Have Cores : 20
UseCores : 1
nu0= 0.200000
Open MP enabled
Have Cores : 20
UseCores : 1
lambda0 : 1.600000
Done
47 allele specific expressed (ASE) genes found and written in file ISoLDE_result_ASE_04-13-2019_03-21-23.tsv.
6089 biallelic (BA) genes found and written in file ISoLDE_result_BA_04-13-2019_03-21-23.tsv.
41 Undetermined (UN) genes found and written in file ISoLDE_result_UN_04-13-2019_03-21-23.tsv.
Among these undetermined (UN) genes, 19 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_04-13-2019_03-21-25.tsv.
4622 biallelic (BA) genes found and written in file ISoLDE_result_BA_04-13-2019_03-21-25.tsv.
1330 Undetermined (UN) genes found and written in file ISoLDE_result_UN_04-13-2019_03-21-25.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
153.56 0.65 154.23
|
ISoLDE.Rcheck/tests_x64/testsIsolde.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 : 20
UseCores : 1
nu0= 0.100000
Open MP enabled
Have Cores : 20
UseCores : 1
lambda0 : 1.600000
Open MP enabled
Have Cores : 20
UseCores : 1
nu0= 0.100000
Open MP enabled
Have Cores : 20
UseCores : 1
lambda0 : 1.600000
Open MP enabled
Have Cores : 20
UseCores : 1
nu0= 0.100000
Open MP enabled
Have Cores : 20
UseCores : 1
lambda0 : 1.600000
Done
45 allele specific expressed (ASE) genes found and written in file ISoLDE_result_ASE_04-13-2019_03-22-37.tsv.
6092 biallelic (BA) genes found and written in file ISoLDE_result_BA_04-13-2019_03-22-37.tsv.
40 Undetermined (UN) genes found and written in file ISoLDE_result_UN_04-13-2019_03-22-37.tsv.
Among these undetermined (UN) genes, 20 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_04-13-2019_03-22-39.tsv.
4622 biallelic (BA) genes found and written in file ISoLDE_result_BA_04-13-2019_03-22-39.tsv.
1330 Undetermined (UN) genes found and written in file ISoLDE_result_UN_04-13-2019_03-22-39.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
73.46 0.54 74.09
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ISoLDE.Rcheck/examples_i386/ISoLDE-Ex.timings
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ISoLDE.Rcheck/examples_x64/ISoLDE-Ex.timings
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