Reed Sorenson
| Snapshot Date: 2024-05-20 14:05:07 -0400 (Mon, 20 May 2024) |
| git_url: https://git.bioconductor.org/packages/RNAdecay |
| git_branch: devel |
| git_last_commit: 95e2395 |
| git_last_commit_date: 2024-04-30 11:53:39 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-22 11:38:10 -0400 (Wed, 22 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4665 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4400 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4427 |
| 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 1730/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RNAdecay 1.25.0 (landing page) Reed Sorenson
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: RNAdecay |
| Version: 1.25.0 |
| 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_1.25.0.tar.gz |
| StartedAt: 2024-05-21 09:35:21 -0400 (Tue, 21 May 2024) |
| EndedAt: 2024-05-21 09:36:26 -0400 (Tue, 21 May 2024) |
| EllapsedTime: 65.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RNAdecay.Rcheck |
| Warnings: 0 |
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###
### 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_1.25.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RNAdecay.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAdecay/DESCRIPTION’ ... OK
* this is package ‘RNAdecay’ version ‘1.25.0’
* 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 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
installed size is 99.8Mb
sub-directories of 1Mb or more:
data 2.7Mb
libs 96.9Mb
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/RNAdecay.Rcheck/00check.log’
for details.
RNAdecay.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RNAdecay
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘RNAdecay’ ...
** 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 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_dExp_1sse -DCPPAD_FRAMEWORK -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general_dExp_1sse.cpp -o general_dExp_1sse.o
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 general_dExp_1sse.so general_dExp_1sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[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 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_Exp_1sse -DCPPAD_FRAMEWORK -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general_Exp_1sse.cpp -o general_Exp_1sse.o
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 general_Exp_1sse.so general_Exp_1sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[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 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_dExp_2sse -DCPPAD_FRAMEWORK -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general_dExp_2sse.cpp -o general_dExp_2sse.o
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 general_dExp_2sse.so general_dExp_2sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[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 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_Exp_2sse -DCPPAD_FRAMEWORK -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general_Exp_2sse.cpp -o general_Exp_2sse.o
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 general_Exp_2sse.so general_Exp_2sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[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 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_dExp_3sse -DCPPAD_FRAMEWORK -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general_dExp_3sse.cpp -o general_dExp_3sse.o
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 general_dExp_3sse.so general_dExp_3sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[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 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_Exp_3sse -DCPPAD_FRAMEWORK -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general_Exp_3sse.cpp -o general_Exp_3sse.o
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 general_Exp_3sse.so general_Exp_3sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[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 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_dExp_4sse -DCPPAD_FRAMEWORK -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general_dExp_4sse.cpp -o general_dExp_4sse.o
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 general_dExp_4sse.so general_dExp_4sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[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 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/TMB/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_Exp_4sse -DCPPAD_FRAMEWORK -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c general_Exp_4sse.cpp -o general_Exp_4sse.o
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 general_Exp_4sse.so general_Exp_4sse.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
[1] 0
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/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)
RNAdecay.Rcheck/RNAdecay-Ex.timings
| name | user | system | elapsed | |
| a_high | 0.001 | 0.001 | 0.001 | |
| aic | 0.000 | 0.001 | 0.001 | |
| cols | 0.007 | 0.002 | 0.011 | |
| comb_cv | 0.003 | 0.000 | 0.004 | |
| const_decay | 0.000 | 0.001 | 0.001 | |
| constraint_fun_list_maker | 0.004 | 0.002 | 0.006 | |
| decay_plot | 2.408 | 0.115 | 2.825 | |
| fit_var | 0.000 | 0.001 | 0.000 | |
| group_map | 0.106 | 0.014 | 0.137 | |
| groupings | 0.004 | 0.002 | 0.006 | |
| hl_plot | 3.070 | 0.029 | 3.563 | |
| log_lik | 0.000 | 0.000 | 0.001 | |
| mod_optimization | 3.019 | 0.145 | 3.628 | |
| n_par | 0.001 | 0.001 | 0.002 | |
| plain_theme | 0.181 | 0.018 | 0.220 | |
| sse_null_decaying_decay | 0.001 | 0.001 | 0.002 | |