Aaron Taudt
| Snapshot Date: 2024-05-26 14:00:09 -0400 (Sun, 26 May 2024) |
| git_url: https://git.bioconductor.org/packages/methimpute |
| git_branch: RELEASE_3_19 |
| git_last_commit: 515e616 |
| git_last_commit_date: 2024-04-30 11:01:18 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-27 11:35:56 -0400 (Mon, 27 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4752 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4517 |
| 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 1228/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methimpute 1.26.0 (landing page) Aaron Taudt
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.26.0 |
| 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_1.26.0.tar.gz |
| StartedAt: 2024-05-26 22:23:42 -0400 (Sun, 26 May 2024) |
| EndedAt: 2024-05-26 22:26:35 -0400 (Sun, 26 May 2024) |
| EllapsedTime: 172.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: methimpute.Rcheck |
| Warnings: 1 |
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### Running command:
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### /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_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/methimpute.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methimpute/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methimpute’ version ‘1.26.0’
* 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 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-3.19-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 20.540 0.383 21.044
extractCytosinesFromFASTA 5.939 0.138 6.117
* 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-3.19-bioc/meat/methimpute.Rcheck/00check.log’
for details.
methimpute.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL methimpute
###
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* 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 | 0.064 | 0.002 | 0.067 | |
| arabidopsis_chromosomes | 0.004 | 0.002 | 0.005 | |
| arabidopsis_genes | 0.023 | 0.003 | 0.025 | |
| arabidopsis_toydata | 0.184 | 0.010 | 0.196 | |
| binning | 3.322 | 0.224 | 3.568 | |
| binomialTestMethylation | 0.239 | 0.011 | 0.253 | |
| callMethylation | 3.097 | 0.120 | 3.236 | |
| callMethylationSeparate | 4.298 | 0.185 | 4.518 | |
| collapseBins | 2.989 | 0.076 | 3.088 | |
| distanceCorrelation | 1.435 | 0.060 | 1.504 | |
| estimateTransDist | 1.478 | 0.048 | 1.534 | |
| exportMethylome | 0 | 0 | 0 | |
| extractCytosinesFromFASTA | 5.939 | 0.138 | 6.117 | |
| getDistinctColors | 0.032 | 0.007 | 0.039 | |
| getStateColors | 0.016 | 0.001 | 0.017 | |
| import | 0.936 | 0.084 | 1.032 | |
| importRene | 0.048 | 0.003 | 0.052 | |
| inflateMethylome | 0.432 | 0.040 | 0.476 | |
| loadFromFiles | 0.141 | 0.003 | 0.145 | |
| plotting | 20.540 | 0.383 | 21.044 | |