Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1217/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methimpute 1.28.0 (landing page) Aaron Taudt
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the methimpute package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methimpute.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: methimpute |
Version: 1.28.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methimpute.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methimpute_1.28.0.tar.gz |
StartedAt: 2024-11-19 23:52:13 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 23:58:01 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 348.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: methimpute.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methimpute.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methimpute_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/methimpute.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘methimpute/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘methimpute’ version ‘1.28.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘methimpute’ can be installed ... WARNING Found the following significant warnings: densities.cpp:920:91: warning: format specifies type 'int' but the argument has type 'double' [-Wformat] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/methimpute.Rcheck/00install.out’ for details. * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: INITIAL RELEASE * 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 ... NOTE checkRd: (-1) methimputeBinomialHMM.Rd:20: Lost braces in \itemize; meant \describe ? checkRd: (-1) methimputeBinomialHMM.Rd:21: Lost braces in \itemize; meant \describe ? checkRd: (-1) methimputeBinomialHMM.Rd:22: Lost braces in \itemize; meant \describe ? checkRd: (-1) methimputeBinomialHMM.Rd:23: Lost braces in \itemize; meant \describe ? checkRd: (-1) methimputeBinomialHMM.Rd:24: Lost braces in \itemize; meant \describe ? checkRd: (-1) methimputeBinomialHMM.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) methimputeBinomialHMM.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) methimputeBinomialHMM.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) methimputeBinomialHMM.Rd:28: Lost braces in \itemize; meant \describe ? * 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 is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotting 14.296 0.257 14.611 * 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: 1 WARNING, 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/methimpute.Rcheck/00check.log’ for details.
methimpute.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL methimpute ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘methimpute’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c densities.cpp -o densities.o In file included from densities.cpp:1: ./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(int test, int total); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2) virtual double getLogDensityAt(int) { return(0); }; ^ ./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(double x); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double') virtual double getLogDensityAt(int) { return(0); }; ^ densities.cpp:920:91: warning: format specifies type 'int' but the argument has type 'double' [-Wformat] if (verbosity>=4) Rprintf(" lGammaR = %g, lgamma(size + obs=%d) = %g\n", lGammaR, obs_j, lgamma(size + obs_j)); ~~ ^~~~~ %f 3 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fitHMM.cpp -o fitHMM.o In file included from fitHMM.cpp:2: In file included from ./scalehmm.h:4: ./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(int test, int total); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2) virtual double getLogDensityAt(int) { return(0); }; ^ ./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(double x); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double') virtual double getLogDensityAt(int) { return(0); }; ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fitHMM_context.cpp -o fitHMM_context.o In file included from fitHMM_context.cpp:2: In file included from ./hmm_context.h:4: ./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(int test, int total); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2) virtual double getLogDensityAt(int) { return(0); }; ^ ./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(double x); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double') virtual double getLogDensityAt(int) { return(0); }; ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmm_context.cpp -o hmm_context.o In file included from hmm_context.cpp:1: In file included from ./hmm_context.h:4: ./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(int test, int total); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2) virtual double getLogDensityAt(int) { return(0); }; ^ ./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(double x); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double') virtual double getLogDensityAt(int) { return(0); }; ^ 2 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c methimpute_init.c -o methimpute_init.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scalehmm.cpp -o scalehmm.o In file included from scalehmm.cpp:1: In file included from ./scalehmm.h:4: ./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(int test, int total); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2) virtual double getLogDensityAt(int) { return(0); }; ^ ./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual] double getLogDensityAt(double x); ^ ./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double') virtual double getLogDensityAt(int) { return(0); }; ^ 2 warnings generated. clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o methimpute.so RcppExports.o densities.o fitHMM.o fitHMM_context.o hmm_context.o methimpute_init.o scalehmm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-methimpute/00new/methimpute/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (methimpute)
methimpute.Rcheck/methimpute-Ex.timings
name | user | system | elapsed | |
arabidopsis_TEs | 0.049 | 0.003 | 0.053 | |
arabidopsis_chromosomes | 0.002 | 0.002 | 0.004 | |
arabidopsis_genes | 0.014 | 0.001 | 0.016 | |
arabidopsis_toydata | 0.132 | 0.008 | 0.140 | |
binning | 2.564 | 0.189 | 2.769 | |
binomialTestMethylation | 0.191 | 0.012 | 0.206 | |
callMethylation | 2.915 | 0.107 | 3.038 | |
callMethylationSeparate | 3.821 | 0.155 | 4.008 | |
collapseBins | 2.071 | 0.046 | 2.127 | |
distanceCorrelation | 1.024 | 0.042 | 1.071 | |
estimateTransDist | 1.086 | 0.031 | 1.123 | |
exportMethylome | 0 | 0 | 0 | |
extractCytosinesFromFASTA | 4.243 | 0.095 | 4.352 | |
getDistinctColors | 0.018 | 0.001 | 0.019 | |
getStateColors | 0.012 | 0.001 | 0.013 | |
import | 0.685 | 0.070 | 0.762 | |
importRene | 0.040 | 0.002 | 0.043 | |
inflateMethylome | 0.319 | 0.035 | 0.356 | |
loadFromFiles | 0.120 | 0.007 | 0.128 | |
plotting | 14.296 | 0.257 | 14.611 | |