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 12:07 -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 1884/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scMET 1.8.0 (landing page) Andreas C. Kapourani
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the scMET package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scMET.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: scMET |
Version: 1.8.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scMET.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scMET_1.8.0.tar.gz |
StartedAt: 2024-11-20 02:24:02 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 02:30:26 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 384.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scMET.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scMET.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scMET_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scMET.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 ‘scMET/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘scMET’ version ‘1.8.0’ * package encoding: UTF-8 * 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 ‘scMET’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... OK Not all R platforms support C++17 * 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 whether startup messages can be suppressed ... 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) scmet_differential.Rd:70: Lost braces; missing escapes or markup? 70 | calibration is performed, and `alpha_{E}`` is set to | ^ * 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 shell scripts ... 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 ... NOTE GNU make is a SystemRequirements. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed scmet_plot_estimated_vs_true 14.479 0.237 14.739 scmet 10.815 0.294 11.172 scmet_hvf_lvf 10.444 0.208 10.756 scmet_plot_vf_tail_prob 9.774 0.153 9.988 scmet_plot_efdr_efnr_grid 9.575 0.192 9.809 scmet_plot_mean_var 9.320 0.134 9.462 sce_to_scmet 5.197 0.207 5.421 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/scMET.Rcheck/00check.log’ for details.
scMET.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scMET ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘scMET’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++17 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_scmet.cc -o stanExports_scmet.o In file included from stanExports_scmet.cc:5: In file included from ./stanExports_scmet.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_scmet.cc:5: In file included from ./stanExports_scmet.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_scmet.cc:5: In file included from ./stanExports_scmet.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> { ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? class ops_partials_edge; ^~~~~ struct In file included from stanExports_scmet.cc:5: In file included from ./stanExports_scmet.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] int ret = stan::services::error_codes::CONFIG; ^ In file included from stanExports_scmet.cc:5: ./stanExports_scmet.h:808:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits<int>::min(); ^ In file included from stanExports_scmet.cc:5: In file included from ./stanExports_scmet.h:9: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] const T x_extrema = 1 / (1 + a); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here temme_root_finder<T>(-lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here rx = detail::ibeta_inv_imp( ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ 6 warnings generated. clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o scMET.so RcppExports.o stanExports_scmet.o -L/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/lib -ltbb -ltbbmalloc -L/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -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-scMET/00new/scMET/libs ** R ** data *** moving datasets to lazyload DB ** 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 (scMET)
scMET.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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(scMET) > > test_check("scMET") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ] > > proc.time() user system elapsed 3.107 0.248 3.153
scMET.Rcheck/scMET-Ex.timings
name | user | system | elapsed | |
bb_mle | 0.059 | 0.004 | 0.064 | |
create_design_matrix | 0.002 | 0.000 | 0.002 | |
sce_to_scmet | 5.197 | 0.207 | 5.421 | |
scmet | 10.815 | 0.294 | 11.172 | |
scmet_differential | 0.000 | 0.000 | 0.001 | |
scmet_hvf_lvf | 10.444 | 0.208 | 10.756 | |
scmet_plot_efdr_efnr_grid | 9.575 | 0.192 | 9.809 | |
scmet_plot_estimated_vs_true | 14.479 | 0.237 | 14.739 | |
scmet_plot_ma | 0 | 0 | 0 | |
scmet_plot_mean_var | 9.320 | 0.134 | 9.462 | |
scmet_plot_vf_tail_prob | 9.774 | 0.153 | 9.988 | |
scmet_plot_volcano | 0 | 0 | 0 | |
scmet_simulate | 0.012 | 0.002 | 0.014 | |
scmet_simulate_diff | 0.027 | 0.000 | 0.028 | |
scmet_to_sce | 0.054 | 0.001 | 0.054 | |