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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1770/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAdecay 1.26.0  (landing page)
Reed Sorenson
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/RNAdecay
git_branch: RELEASE_3_20
git_last_commit: 908ebd3
git_last_commit_date: 2024-10-29 11:26:41 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for RNAdecay on nebbiolo2

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: 1.26.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RNAdecay.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RNAdecay_1.26.0.tar.gz
StartedAt: 2024-12-20 04:50:33 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 04:55:09 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 276.3 seconds
RetCode: 0
Status:   OK  
CheckDir: RNAdecay.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RNAdecay.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RNAdecay_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘RNAdecay/DESCRIPTION’ ... OK
* this is package ‘RNAdecay’ version ‘1.26.0’
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... NOTE
  installed size is 233.1Mb
  sub-directories of 1Mb or more:
    data    2.7Mb
    libs  230.3Mb
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay.Rcheck/00check.log’
for details.


Installation output

RNAdecay.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL RNAdecay
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘RNAdecay’ ...
** using staged installation
** libs
/home/biocbuild/bbs-3.20-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay/src'
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.20-bioc/R/site-library/TMB/include" -I"/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_dExp_1sse  -DCPPAD_FRAMEWORK  -I/usr/local/include    -fpic  -g -O2  -Wall  -c general_dExp_1sse.cpp -o general_dExp_1sse.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o general_dExp_1sse.so general_dExp_1sse.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay/src'
[1] 0
/home/biocbuild/bbs-3.20-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay/src'
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.20-bioc/R/site-library/TMB/include" -I"/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_Exp_1sse  -DCPPAD_FRAMEWORK  -I/usr/local/include    -fpic  -g -O2  -Wall  -c general_Exp_1sse.cpp -o general_Exp_1sse.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o general_Exp_1sse.so general_Exp_1sse.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay/src'
[1] 0
/home/biocbuild/bbs-3.20-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay/src'
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.20-bioc/R/site-library/TMB/include" -I"/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_dExp_2sse  -DCPPAD_FRAMEWORK  -I/usr/local/include    -fpic  -g -O2  -Wall  -c general_dExp_2sse.cpp -o general_dExp_2sse.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o general_dExp_2sse.so general_dExp_2sse.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay/src'
[1] 0
/home/biocbuild/bbs-3.20-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay/src'
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.20-bioc/R/site-library/TMB/include" -I"/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_Exp_2sse  -DCPPAD_FRAMEWORK  -I/usr/local/include    -fpic  -g -O2  -Wall  -c general_Exp_2sse.cpp -o general_Exp_2sse.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o general_Exp_2sse.so general_Exp_2sse.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay/src'
[1] 0
/home/biocbuild/bbs-3.20-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay/src'
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.20-bioc/R/site-library/TMB/include" -I"/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_dExp_3sse  -DCPPAD_FRAMEWORK  -I/usr/local/include    -fpic  -g -O2  -Wall  -c general_dExp_3sse.cpp -o general_dExp_3sse.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o general_dExp_3sse.so general_dExp_3sse.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay/src'
[1] 0
/home/biocbuild/bbs-3.20-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay/src'
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.20-bioc/R/site-library/TMB/include" -I"/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_Exp_3sse  -DCPPAD_FRAMEWORK  -I/usr/local/include    -fpic  -g -O2  -Wall  -c general_Exp_3sse.cpp -o general_Exp_3sse.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o general_Exp_3sse.so general_Exp_3sse.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay/src'
[1] 0
/home/biocbuild/bbs-3.20-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay/src'
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.20-bioc/R/site-library/TMB/include" -I"/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_dExp_4sse  -DCPPAD_FRAMEWORK  -I/usr/local/include    -fpic  -g -O2  -Wall  -c general_dExp_4sse.cpp -o general_dExp_4sse.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o general_dExp_4sse.so general_dExp_4sse.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay/src'
[1] 0
/home/biocbuild/bbs-3.20-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay/src'
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.20-bioc/R/site-library/TMB/include" -I"/home/biocbuild/bbs-3.20-bioc/R/site-library/RcppEigen/include"   -DTMB_EIGEN_DISABLE_WARNINGS   -DTMB_LIB_INIT=R_init_general_Exp_4sse  -DCPPAD_FRAMEWORK  -I/usr/local/include    -fpic  -g -O2  -Wall  -c general_Exp_4sse.cpp -o general_Exp_4sse.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o general_Exp_4sse.so general_Exp_4sse.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/RNAdecay/src'
[1] 0
installing to /home/biocbuild/bbs-3.20-bioc/R/site-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_high000
aic0.0000.0000.001
cols0.0020.0000.002
comb_cv0.0010.0000.001
const_decay0.0000.0000.001
constraint_fun_list_maker0.0020.0000.002
decay_plot0.9440.0310.975
fit_var000
group_map0.0410.0010.041
groupings0.0010.0000.001
hl_plot1.1760.0261.202
log_lik0.0000.0000.001
mod_optimization1.2490.0791.329
n_par0.0010.0000.000
plain_theme0.0640.0010.065
sse_null_decaying_decay0.0000.0000.001