Aaron Taudt
| Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/methimpute |
| git_branch: RELEASE_3_18 |
| git_last_commit: 3309a71 |
| git_last_commit_date: 2023-10-24 11:00:17 -0400 (Tue, 24 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:13 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 1217/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| methimpute 1.24.0 (landing page) Aaron Taudt
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the methimpute package: - 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: 1.24.0 |
| 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_1.24.0.tar.gz |
| StartedAt: 2024-04-17 18:56:11 -0400 (Wed, 17 Apr 2024) |
| EndedAt: 2024-04-17 18:58:57 -0400 (Wed, 17 Apr 2024) |
| EllapsedTime: 165.5 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_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/methimpute.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘methimpute/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘methimpute’ version ‘1.24.0’
* 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:
hmm_context.cpp:168:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
hmm_context.cpp:469:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
scalehmm.cpp:411:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
scalehmm.cpp:593:13: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
scalehmm.cpp:726:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/methimpute.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* 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 R 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 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 16.759 0.309 17.132
extractCytosinesFromFASTA 5.410 0.110 5.523
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/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/4.3-arm64/Resources/library’
* installing *source* package ‘methimpute’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/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); };
^
2 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/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 arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/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 arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/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); };
^
hmm_context.cpp:168:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
else if ((this->emissionDensities[0]->get_name() == NEGATIVE_BINOMIAL) | (this->emissionDensities[0]->get_name() == ZERO_INFLATION))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
hmm_context.cpp:168:12: note: cast one or both operands to int to silence this warning
hmm_context.cpp:469:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
else if ((this->emissionDensities[0]->get_name() == NEGATIVE_BINOMIAL) | (this->emissionDensities[0]->get_name() == ZERO_INFLATION))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
hmm_context.cpp:469:12: note: cast one or both operands to int to silence this warning
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c methimpute_init.c -o methimpute_init.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/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); };
^
scalehmm.cpp:411:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
else if ((this->emissionDensities[0]->get_name() == NEGATIVE_BINOMIAL) | (this->emissionDensities[0]->get_name() == ZERO_INFLATION))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
scalehmm.cpp:411:12: note: cast one or both operands to int to silence this warning
scalehmm.cpp:593:13: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
else if ((this->emissionDensities[0]->get_name() == NEGATIVE_BINOMIAL) | (this->emissionDensities[0]->get_name() == ZERO_INFLATION))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
scalehmm.cpp:593:13: note: cast one or both operands to int to silence this warning
scalehmm.cpp:726:12: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
else if ((this->emissionDensities[0]->get_name() == NEGATIVE_BINOMIAL) | (this->emissionDensities[0]->get_name() == ZERO_INFLATION))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
scalehmm.cpp:726:12: note: cast one or both operands to int to silence this warning
5 warnings generated.
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.3-arm64/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 | 0.060 | 0.004 | 0.066 | |
| arabidopsis_chromosomes | 0.004 | 0.003 | 0.007 | |
| arabidopsis_genes | 0.021 | 0.003 | 0.025 | |
| arabidopsis_toydata | 0.205 | 0.009 | 0.218 | |
| binning | 3.156 | 0.147 | 3.321 | |
| binomialTestMethylation | 0.301 | 0.004 | 0.305 | |
| callMethylation | 3.612 | 0.077 | 3.690 | |
| callMethylationSeparate | 4.382 | 0.127 | 4.519 | |
| collapseBins | 2.284 | 0.038 | 2.323 | |
| distanceCorrelation | 1.402 | 0.051 | 1.453 | |
| estimateTransDist | 1.819 | 0.048 | 1.867 | |
| exportMethylome | 0 | 0 | 0 | |
| extractCytosinesFromFASTA | 5.410 | 0.110 | 5.523 | |
| getDistinctColors | 0.027 | 0.001 | 0.030 | |
| getStateColors | 0.013 | 0.001 | 0.013 | |
| import | 0.563 | 0.044 | 0.611 | |
| importRene | 0.044 | 0.003 | 0.047 | |
| inflateMethylome | 0.543 | 0.054 | 0.596 | |
| loadFromFiles | 0.212 | 0.003 | 0.214 | |
| plotting | 16.759 | 0.309 | 17.132 | |