Reed Sorenson
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/RNAdecay |
| git_branch: RELEASE_3_16 |
| git_last_commit: 3619ad8 |
| git_last_commit_date: 2022-11-01 11:17:45 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:17 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the RNAdecay package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1699/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RNAdecay 1.18.0 (landing page) Reed Sorenson
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: RNAdecay |
| Version: 1.18.0 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:RNAdecay.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings RNAdecay_1.18.0.tar.gz |
| StartedAt: 2023-04-10 23:30:03 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 23:32:55 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 172.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RNAdecay.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:RNAdecay.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings RNAdecay_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘RNAdecay/DESCRIPTION’ ... OK
* this is package ‘RNAdecay’ version ‘1.18.0’
* 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
* checking installed package size ... NOTE
installed size is 129.6Mb
sub-directories of 1Mb or more:
data 2.7Mb
libs 126.6Mb
* 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 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘RNAdecay_workflow.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay.Rcheck/00check.log’
for details.
RNAdecay.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL RNAdecay
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘RNAdecay’ ...
** using staged installation
** libs
** arch -
/home/biocbuild/bbs-3.16-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)"
make[1]: Entering directory '/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay/src'
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.16-bioc/R/site-library/TMB/include" -I"/home/biocbuild/bbs-3.16-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++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o general_dExp_1sse.so general_dExp_1sse.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
make[1]: Leaving directory '/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay/src'
[1] 0
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.5.3
Current Matrix version is 1.5.4
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
/home/biocbuild/bbs-3.16-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)"
make[1]: Entering directory '/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay/src'
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.16-bioc/R/site-library/TMB/include" -I"/home/biocbuild/bbs-3.16-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++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o general_Exp_1sse.so general_Exp_1sse.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
make[1]: Leaving directory '/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay/src'
[1] 0
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.5.3
Current Matrix version is 1.5.4
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
/home/biocbuild/bbs-3.16-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)"
make[1]: Entering directory '/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay/src'
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.16-bioc/R/site-library/TMB/include" -I"/home/biocbuild/bbs-3.16-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++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o general_dExp_2sse.so general_dExp_2sse.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
make[1]: Leaving directory '/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay/src'
[1] 0
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.5.3
Current Matrix version is 1.5.4
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
/home/biocbuild/bbs-3.16-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)"
make[1]: Entering directory '/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay/src'
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.16-bioc/R/site-library/TMB/include" -I"/home/biocbuild/bbs-3.16-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++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o general_Exp_2sse.so general_Exp_2sse.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
make[1]: Leaving directory '/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay/src'
[1] 0
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.5.3
Current Matrix version is 1.5.4
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
/home/biocbuild/bbs-3.16-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)"
make[1]: Entering directory '/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay/src'
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.16-bioc/R/site-library/TMB/include" -I"/home/biocbuild/bbs-3.16-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++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o general_dExp_3sse.so general_dExp_3sse.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
make[1]: Leaving directory '/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay/src'
[1] 0
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.5.3
Current Matrix version is 1.5.4
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
/home/biocbuild/bbs-3.16-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)"
make[1]: Entering directory '/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay/src'
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.16-bioc/R/site-library/TMB/include" -I"/home/biocbuild/bbs-3.16-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++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o general_Exp_3sse.so general_Exp_3sse.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
make[1]: Leaving directory '/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay/src'
[1] 0
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.5.3
Current Matrix version is 1.5.4
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
/home/biocbuild/bbs-3.16-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)"
make[1]: Entering directory '/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay/src'
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.16-bioc/R/site-library/TMB/include" -I"/home/biocbuild/bbs-3.16-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++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o general_dExp_4sse.so general_dExp_4sse.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
make[1]: Leaving directory '/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay/src'
[1] 0
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.5.3
Current Matrix version is 1.5.4
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
/home/biocbuild/bbs-3.16-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)"
make[1]: Entering directory '/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay/src'
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.16-bioc/R/site-library/TMB/include" -I"/home/biocbuild/bbs-3.16-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++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o general_Exp_4sse.so general_Exp_4sse.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
make[1]: Leaving directory '/home/biocbuild/bbs-3.16-bioc/meat/RNAdecay/src'
[1] 0
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.5.3
Current Matrix version is 1.5.4
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
installing to /home/biocbuild/bbs-3.16-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)
RNAdecay.Rcheck/RNAdecay-Ex.timings
| name | user | system | elapsed | |
| a_high | 0.000 | 0.000 | 0.001 | |
| aic | 0 | 0 | 0 | |
| cols | 0.003 | 0.000 | 0.003 | |
| comb_cv | 0.002 | 0.000 | 0.002 | |
| const_decay | 0 | 0 | 0 | |
| constraint_fun_list_maker | 0.001 | 0.000 | 0.001 | |
| decay_plot | 1.017 | 0.024 | 1.041 | |
| fit_var | 0 | 0 | 0 | |
| group_map | 0.042 | 0.000 | 0.043 | |
| groupings | 0.001 | 0.000 | 0.001 | |
| hl_plot | 1.193 | 0.072 | 1.266 | |
| log_lik | 0.001 | 0.000 | 0.001 | |
| mod_optimization | 1.391 | 0.072 | 1.464 | |
| n_par | 0.001 | 0.000 | 0.001 | |
| plain_theme | 0.258 | 0.000 | 0.258 | |
| sse_null_decaying_decay | 0 | 0 | 0 | |