Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1046/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ISoLDE 1.33.0 (landing page) Christelle Reynès
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the ISoLDE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ISoLDE.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: ISoLDE |
Version: 1.33.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ISoLDE.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ISoLDE_1.33.0.tar.gz |
StartedAt: 2024-06-10 04:21:46 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 04:24:33 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 166.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ISoLDE.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ISoLDE.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ISoLDE_1.33.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ISoLDE.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'ISoLDE/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ISoLDE' version '1.33.0' * 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 whether package 'ISoLDE' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * 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 code 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/ISoLDE/libs/x64/ISoLDE.dll': Found '_assert', possibly from 'assert' (C) Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) 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 nor [v]sprintf. 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 ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testsIsolde.R' OK * checking package vignettes ... NOTE Package has 'vignettes' subdirectory but apparently no vignettes. Perhaps the 'VignetteBuilder' information is missing from the DESCRIPTION file? * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/ISoLDE.Rcheck/00check.log' for details.
ISoLDE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ISoLDE ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'ISoLDE' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Isolde.c -o Isolde.o gcc -shared -s -static-libgcc -o ISoLDE.dll tmp.def Isolde.o -fopenmp -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-ISoLDE/00new/ISoLDE/libs/x64 ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ISoLDE)
ISoLDE.Rcheck/tests/testsIsolde.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 : 32 UseCores : 1 nu0= 0.200000 Open MP enabled Have Cores : 32 UseCores : 1 lambda0 : 1.600000 Open MP enabled Have Cores : 32 UseCores : 1 nu0= 0.100000 Open MP enabled Have Cores : 32 UseCores : 1 lambda0 : 1.600000 Open MP enabled Have Cores : 32 UseCores : 1 nu0= 0.200000 Open MP enabled Have Cores : 32 UseCores : 1 lambda0 : 1.600000 Done 51 allele specific expressed (ASE) genes found and written in file ISoLDE_result_ASE_06-10-2024_04-24-18.tsv. 6084 biallelic (BA) genes found and written in file ISoLDE_result_BA_06-10-2024_04-24-18.tsv. 42 Undetermined (UN) genes found and written in file ISoLDE_result_UN_06-10-2024_04-24-18.tsv. Among these undetermined (UN) genes, 21 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_06-10-2024_04-24-19.tsv. 4622 biallelic (BA) genes found and written in file ISoLDE_result_BA_06-10-2024_04-24-19.tsv. 1330 Undetermined (UN) genes found and written in file ISoLDE_result_UN_06-10-2024_04-24-19.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 47.71 2.39 50.12
ISoLDE.Rcheck/ISoLDE-Ex.timings
name | user | system | elapsed | |
filterT | 0.48 | 0.28 | 0.77 | |
filteredASRcounts | 0.03 | 0.00 | 0.03 | |
isolde_test | 1.42 | 0.08 | 1.50 | |
normASRcounts | 0.47 | 0.03 | 0.55 | |
rawASRcounts | 0.11 | 0.02 | 0.14 | |
readNormInput | 0.3 | 0.0 | 0.3 | |
readRawInput | 0.11 | 0.00 | 0.11 | |
readTarget | 0.06 | 0.01 | 0.09 | |