Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2135/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TFBSTools 1.44.0 (landing page) Ge Tan
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the TFBSTools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TFBSTools.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: TFBSTools |
Version: 1.44.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TFBSTools.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TFBSTools_1.44.0.tar.gz |
StartedAt: 2024-12-20 06:42:28 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 06:49:51 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 442.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TFBSTools.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TFBSTools.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TFBSTools_1.44.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/TFBSTools.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'TFBSTools/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'TFBSTools' version '1.44.0' * 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 'TFBSTools' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.3.0' * checking installed package size ... OK * checking package directory ... OK * checking 'build' 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 ... NOTE Unexported objects imported by ':::' calls: 'S4Vectors:::new_SimpleList_from_list' 'seqLogo:::pwm2ic' See the note in ?`:::` about the use of this operator. * 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 LazyData ... 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/TFBSTools/libs/x64/TFBSTools.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (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' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed SiteSetList-class 43.39 0.36 43.75 searchAln-methods 13.09 0.18 13.42 toGRangesList-methods 8.44 0.13 8.61 SiteSet-class 5.88 0.42 6.29 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/TFBSTools.Rcheck/00check.log' for details.
TFBSTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL TFBSTools ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'TFBSTools' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matrixAlignerDynamic.c -o matrixAlignerDynamic.o matrixAlignerDynamic.c: In function 'score': matrixAlignerDynamic.c:235:22: warning: 'best_pntr' may be used uninitialized [-Wmaybe-uninitialized] 235 | while (current_pntr->father != NULL){ // while the father of the current pointer exists, walk through the best posible alignment | ~~~~~~~~~~~~^~~~~~~~ matrixAlignerDynamic.c:115:17: note: 'best_pntr' was declared here 115 | struct entry *best_pntr; // pointer to the best entry so far | ^~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_TFBSTools.c -o R_init_TFBSTools.o gcc -shared -s -static-libgcc -o TFBSTools.dll tmp.def matrixAlignerDynamic.o R_init_TFBSTools.o -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-TFBSTools/00new/TFBSTools/libs/x64 ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for 'seqLogo' in package 'TFBSTools' Creating a generic function for 'colSums' from package 'base' in package 'TFBSTools' Creating a generic function for 'rowSums' from package 'base' in package 'TFBSTools' ** 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 (TFBSTools)
TFBSTools.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 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(testthat) > library(TFBSTools) > > test_check("TFBSTools") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ] > > proc.time() user system elapsed 18.03 1.17 20.36
TFBSTools.Rcheck/TFBSTools-Ex.timings
name | user | system | elapsed | |
IUPAC2Matrix | 0 | 0 | 0 | |
MA0004.1 | 0.00 | 0.02 | 0.01 | |
MotifSet-class | 0 | 0 | 0 | |
PFMSimilarity-methods | 0.20 | 0.09 | 0.38 | |
PWMSimilarity-methods | 0.01 | 0.00 | 0.02 | |
SiteSet-class | 5.88 | 0.42 | 6.29 | |
SiteSetList-class | 43.39 | 0.36 | 43.75 | |
TFFM-class | 0.02 | 0.00 | 0.05 | |
XMatrix-class | 0.01 | 0.00 | 0.01 | |
XMatrixList-class | 0.02 | 0.03 | 0.05 | |
deleteMatrixHavingID-methods | 0.03 | 0.08 | 0.28 | |
dmmEM-methods | 0 | 0 | 0 | |
getEmissionProb | 0.22 | 0.00 | 0.27 | |
getMatrixByID-methods | 0.22 | 0.03 | 0.87 | |
getMatrixSet-methods | 0 | 0 | 0 | |
getPosProb | 0.16 | 0.00 | 0.15 | |
makeFlatFileDir | 0 | 0 | 0 | |
parseMEMEOutput | 0.23 | 0.00 | 0.25 | |
permuteMatrix-methods | 0.1 | 0.0 | 0.1 | |
rPWMDmm-methods | 0 | 0 | 0 | |
readJASPARMatrix | 0.00 | 0.02 | 0.07 | |
readXMLTFFM | 0.03 | 0.00 | 0.04 | |
runMEME-methods | 0 | 0 | 0 | |
sampleRanges | 0.38 | 0.01 | 0.39 | |
searchAln-methods | 13.09 | 0.18 | 13.42 | |
searchPairBSgenome-methods | 0 | 0 | 0 | |
searchSeq-methods | 1.28 | 0.03 | 1.33 | |
seqLogo | 0.77 | 0.20 | 0.97 | |
shannon.entropy | 0 | 0 | 0 | |
toGRangesList-methods | 8.44 | 0.13 | 8.61 | |
toICM-methods | 0.01 | 0.00 | 0.02 | |
toPWM-methods | 0.02 | 0.00 | 0.01 | |