Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-04-22 13:18 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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 1803/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAdecay 1.28.0  (landing page)
Reed Sorenson
Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025)
git_url: https://git.bioconductor.org/packages/RNAdecay
git_branch: RELEASE_3_21
git_last_commit: 0249aee
git_last_commit_date: 2025-04-15 13:26:53 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  

CHECK results for RNAdecay on kjohnson3

To the developers/maintainers of the RNAdecay package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RNAdecay.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.

raw results


Summary

Package: RNAdecay
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RNAdecay.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RNAdecay_1.28.0.tar.gz
StartedAt: 2025-04-21 21:17:09 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 21:17:25 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 16.2 seconds
RetCode: 0
Status:   OK  
CheckDir: RNAdecay.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RNAdecay.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RNAdecay_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RNAdecay.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAdecay/DESCRIPTION’ ... OK
* this is package ‘RNAdecay’ version ‘1.28.0’
* 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 ‘RNAdecay’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... INFO
  installed size is 97.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs  94.8Mb
* 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 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 ... NOTE
decay_plot: no visible binding for global variable ‘text’
decay_plot: no visible binding for global variable ‘x’
decay_plot: no visible binding for global variable ‘y’
decay_plot: no visible binding for global variable ‘treatment’
decay_plot: no visible binding for global variable ‘t.decay’
decay_plot: no visible binding for global variable ‘value’
hl_plot: no visible binding for global variable ‘x’
hl_plot: no visible binding for global variable ‘y’
Undefined global functions or variables:
  t.decay text treatment value x y
Consider adding
  importFrom("graphics", "text")
to your NAMESPACE file.
* 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/RNAdecay.Rcheck/00check.log’
for details.

Installation output

RNAdecay.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RNAdecay
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘RNAdecay’ ...
** this is package ‘RNAdecay’ version ‘1.28.0’
** using staged installation
** libs
/Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_dExp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_dExp_1sse  -DCPPAD_FRAMEWORK  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c general_dExp_1sse.cpp -o general_dExp_1sse.o
In file included from general_dExp_1sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include/TMB.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from general_dExp_1sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include/TMB.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_dExp_1sse.so general_dExp_1sse.o -F/Library/Frameworks/R.framework/.. -framework R
[1] 0
/Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_Exp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_Exp_1sse  -DCPPAD_FRAMEWORK  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c general_Exp_1sse.cpp -o general_Exp_1sse.o
In file included from general_Exp_1sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include/TMB.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from general_Exp_1sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include/TMB.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_Exp_1sse.so general_Exp_1sse.o -F/Library/Frameworks/R.framework/.. -framework R
[1] 0
/Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_dExp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_dExp_2sse  -DCPPAD_FRAMEWORK  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c general_dExp_2sse.cpp -o general_dExp_2sse.o
In file included from general_dExp_2sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include/TMB.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from general_dExp_2sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include/TMB.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_dExp_2sse.so general_dExp_2sse.o -F/Library/Frameworks/R.framework/.. -framework R
[1] 0
/Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_Exp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_Exp_2sse  -DCPPAD_FRAMEWORK  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c general_Exp_2sse.cpp -o general_Exp_2sse.o
In file included from general_Exp_2sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include/TMB.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from general_Exp_2sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include/TMB.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_Exp_2sse.so general_Exp_2sse.o -F/Library/Frameworks/R.framework/.. -framework R
[1] 0
/Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_dExp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_dExp_3sse  -DCPPAD_FRAMEWORK  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c general_dExp_3sse.cpp -o general_dExp_3sse.o
In file included from general_dExp_3sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include/TMB.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from general_dExp_3sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include/TMB.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_dExp_3sse.so general_dExp_3sse.o -F/Library/Frameworks/R.framework/.. -framework R
[1] 0
/Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_Exp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_Exp_3sse  -DCPPAD_FRAMEWORK  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c general_Exp_3sse.cpp -o general_Exp_3sse.o
In file included from general_Exp_3sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include/TMB.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from general_Exp_3sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include/TMB.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_Exp_3sse.so general_Exp_3sse.o -F/Library/Frameworks/R.framework/.. -framework R
[1] 0
/Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_dExp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_dExp_4sse  -DCPPAD_FRAMEWORK  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c general_dExp_4sse.cpp -o general_dExp_4sse.o
In file included from general_dExp_4sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include/TMB.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from general_dExp_4sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include/TMB.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_dExp_4sse.so general_dExp_4sse.o -F/Library/Frameworks/R.framework/.. -framework R
[1] 0
/Library/Frameworks/R.framework/Resources/bin/Rscript --vanilla -e "TMB::compile('general_Exp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_Exp_4sse  -DCPPAD_FRAMEWORK  -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c general_Exp_4sse.cpp -o general_Exp_4sse.o
In file included from general_Exp_4sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include/TMB.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from general_Exp_4sse.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/TMB/include/TMB.hpp:96:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o general_Exp_4sse.so general_Exp_4sse.o -F/Library/Frameworks/R.framework/.. -framework R
[1] 0
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-RNAdecay/00new/RNAdecay/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 (RNAdecay)

Tests output


Example timings

RNAdecay.Rcheck/RNAdecay-Ex.timings

nameusersystemelapsed
a_high0.0000.0000.001
aic000
cols0.0010.0000.001
comb_cv0.0000.0000.001
const_decay0.0010.0010.000
constraint_fun_list_maker0.0000.0000.001
decay_plot0.3860.0190.406
fit_var000
group_map0.0200.0030.024
groupings0.0000.0000.001
hl_plot0.4010.0030.407
log_lik000
mod_optimization0.4790.0190.516
n_par0.0000.0010.001
plain_theme0.0210.0010.023
sse_null_decaying_decay000