Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:16 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the PING package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PING.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1395/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PING 2.36.0 (landing page) Renan Sauteraud
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: PING |
Version: 2.36.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PING.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PING_2.36.0.tar.gz |
StartedAt: 2021-10-15 03:27:40 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 03:33:37 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 357.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: PING.Rcheck |
Warnings: 4 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PING.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PING_2.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/PING.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'PING/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'PING' version '2.36.0' * 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 'PING' can be installed ... WARNING Found the following significant warnings: ping.c:145:40: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/PING.Rcheck/00install.out' for details. * checking installed package size ... NOTE installed size is 8.1Mb sub-directories of 1Mb or more: extdata 5.7Mb libs 1.4Mb * 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 ... NOTE Warning: no function found corresponding to methods exports from 'PING' for: 'show' A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. ** 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 ... NOTE Warning: no function found corresponding to methods exports from 'PING' for: 'show' A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. ** checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: 'BSgenome' 'BiocGenerics' 'GenomicRanges' 'IRanges' 'S4Vectors' 'fda' 'methods' 'stats' 'stats4' All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE plot,ping-segReads: warning in symbols((map[, 1] + map[, 2])/2, rep(0.35, nMap), rectangle = cbind(map[, 2] - map[, 1], rep(0.6, nMap)), inches = FALSE, bg = grey(0.6), fg = 0, add = TRUE, xlim = c(m, M), ylim = c(0, 1)): partial argument match of 'rectangle' to 'rectangles' plot,ping-segReads : <anonymous>: warning in symbols(x@estimates$mu + shift * se(x), rep(0.5, K), rec = matrix(rep(c(147, 0.8), K), ncol = 2, byrow = TRUE), inches = FALSE, bg = 0, fg = grey(abs(shift) * se(x)/(3 * (se(x)))), add = TRUE, xlim = c(m, M), ylim = c(0, 1), lwd = 2): partial argument match of 'rec' to 'rectangles' plot,ping-segReads: warning in symbols(x@estimates$mu, rep(0.5, K), rec = matrix(rep(c(147, 0.8), K), ncol = 2, byrow = TRUE), inches = FALSE, bg = "white", fg = grey(abs(0)), add = TRUE, xlim = c(m, M), ylim = c(0, 1)): partial argument match of 'rec' to 'rectangles' CoverageTrack: no visible global function definition for 'resize' CoverageTrack: no visible global function definition for 'seqnames' CoverageTrack: no visible global function definition for 'start' CoverageTrack: no visible global function definition for 'coverage' CoverageTrack: no visible global function definition for 'width' FilterPING: no visible global function definition for 'quantile' NucleosomeTrack: no visible global function definition for 'as' PostDelta: no visible global function definition for 'head' PostDelta: no visible global function definition for 'as' PostDup: no visible global function definition for 'head' PostDup: no visible global function definition for 'as' PostError: no visible global function definition for 'head' PostError: no visible global function definition for 'summarySeg' PostError: no visible global function definition for 'as' PostSigma: no visible global function definition for 'head' PostSigma: no visible global function definition for 'as' RawReadsTrack: no visible global function definition for 'seqnames' RawReadsTrack: no visible global function definition for 'start' RawReadsTrack: no visible global function definition for 'end' RawReadsTrack: no visible global function definition for 'strand' make.thickthin: no visible global function definition for 'as.roman' newPing: no visible global function definition for 'new' newPingError: no visible global function definition for 'new' newPingList: no visible global function definition for 'new' postPING: no visible global function definition for 'as' segmentPING: no visible global function definition for 'var' segmentPING: no visible global function definition for 'seqlevels' segmentPING: no visible global function definition for 'IRanges' segmentPING: no visible global function definition for 'start' segmentPING: no visible global function definition for 'end' segmentPING: no visible global function definition for 'candidate.region' segmentPING: no visible global function definition for 'segChrRead' segmentPING: no visible global function definition for 'segReadsListPE' truncateResult: no visible global function definition for 'read.table' as.data.frame,pingList: no visible global function definition for 'as' plot,data.frame-data.frame: no visible global function definition for 'pingFDR2' plot,data.frame-data.frame: no visible global function definition for 'tail' plot,data.frame-data.frame: no visible global function definition for 'head' plot,ping-segReads : .densityMix: no visible global function definition for 'dt' plot,ping-segReads: no visible global function definition for 'tail' plot,pingError-segReads: no visible global function definition for 'tail' plot,pingList-pingList: no visible global function definition for 'pingFDR' show,pingList: no visible global function definition for 'getSlots' summary,segReads: no visible global function definition for 'tail' Undefined global functions or variables: IRanges as as.roman candidate.region coverage dt end getSlots head new pingFDR pingFDR2 quantile read.table resize segChrRead segReadsListPE seqlevels seqnames start strand summarySeg tail var width Consider adding importFrom("methods", "as", "getSlots", "new") importFrom("stats", "dt", "end", "quantile", "start", "var") importFrom("utils", "as.roman", "head", "read.table", "tail") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: 'CoverageTrack' 'NucleosomeTrack' 'PING' 'RawReadsTrack' 'makeGRangesOutput' 'newPing' 'newPingError' 'newPingList' 'plotSummary' 'segmentPING' Undocumented S4 classes: 'pingList' 'ping' 'pingError' Undocumented S4 methods: generic '[' and siglist 'pingList,ANY,ANY,ANY' generic 'as.data.frame' and siglist 'pingList' generic 'density' and siglist 'ping' generic 'density' and siglist 'pingError' generic 'density' and siglist 'pingList' generic 'plot' and siglist 'data.frame,data.frame' generic 'plot' and siglist 'ping,segReads' generic 'plot' and siglist 'pingError,segReads' generic 'plot' and siglist 'pingList,pingList' generic 'plot' and siglist 'pingList,segReadsList' generic 'show' and siglist 'pingList' generic 'summary' and siglist 'ping' generic 'summary' and siglist 'pingList' generic 'summary' and siglist 'segReads' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Documented arguments not in \usage in documentation object 'postPING': 'minK' 'maxK' 'tol' 'B' 'mSelect' 'mergePeaks' 'mapCorrect' 'xi' 'rho' 'alpha' 'beta' 'lambda' 'dMu' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... NOTE Package has both 'src/Makevars.in' and 'src/Makevars'. Installation with --no-configure' is unlikely to work. If you intended 'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win' otherwise remove it. If 'configure' created 'src/Makevars', you need a 'cleanup' script. * 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 i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/PING/libs/i386/PING.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/PING/libs/x64/PING.dll': 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. 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': 'PING.Rmd' Package has no Sweave vignette sources and no VignetteBuilder field. * checking examples ... NONE * checking PDF version of manual ... OK * DONE Status: 4 WARNINGs, 7 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/PING.Rcheck/00check.log' for details.
PING.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/PING_2.36.0.tar.gz && rm -rf PING.buildbin-libdir && mkdir PING.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PING.buildbin-libdir PING_2.36.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL PING_2.36.0.zip && rm PING_2.36.0.tar.gz PING_2.36.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 30 4626k 30 1428k 0 0 2209k 0 0:00:02 --:--:-- 0:00:02 2208k 100 4626k 100 4626k 0 0 3309k 0 0:00:01 0:00:01 --:--:-- 3311k install for i386 * installing *source* package 'PING' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/i386/include -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/i386/include -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ping.c -o ping.o ping.c: In function 'fitModelAllk': ping.c:145:40: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] if( REAL(VECTOR_ELT(paraPrior, 5))[0]>0 & REAL(VECTOR_ELT(paraEM, 0))[0]==0) // automatically decide minK and maxKK for histone data, when minK=0 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ ping.c: In function 'ECM2': ping.c:1536:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable] double chiSum = 0, etaF, etaR, dd, cc; ^~~~~~ ping.c: In function 'mergePeak': ping.c:3280:20: warning: variable 'tstatMax' set but not used [-Wunused-but-set-variable] double tstat=0.0,tstatMax=0.0; ^~~~~~~~ ping.c: In function 'fitModelK': ping.c:477:18: warning: 'firstFit' may be used uninitialized in this function [-Wmaybe-uninitialized] SEXP ans, temp, firstFit; ^~~~~~~~ C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o PING.dll tmp.def init.o ping.o -lws2_32 -L/i386/lib -lgsl -lgslcblas -lm -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/PING.buildbin-libdir/00LOCK-PING/00new/PING/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'PING' finding HTML links ... done postPING html ** 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 install for x64 * installing *source* package 'PING' ... ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/src/include -I/x64/include -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ping.c -o ping.o ping.c: In function 'fitModelAllk': ping.c:145:40: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] if( REAL(VECTOR_ELT(paraPrior, 5))[0]>0 & REAL(VECTOR_ELT(paraEM, 0))[0]==0) // automatically decide minK and maxKK for histone data, when minK=0 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ ping.c: In function 'ECM2': ping.c:1536:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable] double chiSum = 0, etaF, etaR, dd, cc; ^~~~~~ ping.c: In function 'mergePeak': ping.c:3280:20: warning: variable 'tstatMax' set but not used [-Wunused-but-set-variable] double tstat=0.0,tstatMax=0.0; ^~~~~~~~ ping.c: In function 'fitModelK': ping.c:477:18: warning: 'firstFit' may be used uninitialized in this function [-Wmaybe-uninitialized] SEXP ans, temp, firstFit; ^~~~~~~~ C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o PING.dll tmp.def init.o ping.o -lws2_32 -L/x64/lib -lgsl -lgslcblas -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/PING.buildbin-libdir/PING/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'PING' as PING_2.36.0.zip * DONE (PING) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'PING' successfully unpacked and MD5 sums checked