| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:37:50 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| 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 1882/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scMET 1.4.0 (landing page) Andreas C. Kapourani
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.4.0 |
| 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_1.4.0.tar.gz |
| StartedAt: 2024-03-03 23:18:38 -0500 (Sun, 03 Mar 2024) |
| EndedAt: 2024-03-03 23:22:26 -0500 (Sun, 03 Mar 2024) |
| EllapsedTime: 228.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scMET.Rcheck |
| Warnings: 0 |
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###
### 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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/scMET.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
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 ‘scMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scMET’ version ‘1.4.0’
* package encoding: UTF-8
* 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 ‘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 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 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 ... 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 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 21.610 0.394 22.169
scmet 16.220 0.442 16.885
scmet_hvf_lvf 15.160 0.327 15.588
scmet_plot_efdr_efnr_grid 14.027 0.338 14.480
scmet_plot_mean_var 13.597 0.280 14.020
scmet_plot_vf_tail_prob 13.028 0.260 13.388
sce_to_scmet 7.517 0.320 7.890
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc/meat/scMET.Rcheck/00check.log’
for details.
scMET.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scMET
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.3-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, const 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 'const 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/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.3-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, const 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 'const 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/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-x86_64/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
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
4.296 0.379 4.447
scMET.Rcheck/scMET-Ex.timings
| name | user | system | elapsed | |
| bb_mle | 0.097 | 0.005 | 0.102 | |
| create_design_matrix | 0.003 | 0.001 | 0.004 | |
| sce_to_scmet | 7.517 | 0.320 | 7.890 | |
| scmet | 16.220 | 0.442 | 16.885 | |
| scmet_differential | 0 | 0 | 0 | |
| scmet_hvf_lvf | 15.160 | 0.327 | 15.588 | |
| scmet_plot_efdr_efnr_grid | 14.027 | 0.338 | 14.480 | |
| scmet_plot_estimated_vs_true | 21.610 | 0.394 | 22.169 | |
| scmet_plot_ma | 0.000 | 0.001 | 0.001 | |
| scmet_plot_mean_var | 13.597 | 0.280 | 14.020 | |
| scmet_plot_vf_tail_prob | 13.028 | 0.260 | 13.388 | |
| scmet_plot_volcano | 0.001 | 0.000 | 0.000 | |
| scmet_simulate | 0.018 | 0.000 | 0.018 | |
| scmet_simulate_diff | 0.733 | 0.027 | 0.763 | |
| scmet_to_sce | 0.164 | 0.002 | 0.166 | |