Reed Sorenson
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/RNAdecay |
| git_branch: RELEASE_3_15 |
| git_last_commit: ae6bfe5 |
| git_last_commit_date: 2022-04-26 11:48:58 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:22:10 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 1672/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RNAdecay 1.16.0 (landing page) Reed Sorenson
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: RNAdecay |
| Version: 1.16.0 |
| Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RNAdecay.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RNAdecay_1.16.0.tar.gz |
| StartedAt: 2022-10-19 03:35:43 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 03:38:40 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 177.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RNAdecay.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RNAdecay.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings RNAdecay_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/RNAdecay.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RNAdecay/DESCRIPTION' ... OK
* this is package 'RNAdecay' version '1.16.0'
* 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 whether package 'RNAdecay' can be installed ... OK
* checking installed package size ... NOTE
installed size is 102.4Mb
sub-directories of 1Mb or more:
data 2.7Mb
libs 99.6Mb
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/RNAdecay/libs/x64/general_Exp_1sse.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'F:/biocbuild/bbs-3.15-bioc/R/library/RNAdecay/libs/x64/general_Exp_2sse.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'F:/biocbuild/bbs-3.15-bioc/R/library/RNAdecay/libs/x64/general_Exp_3sse.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'F:/biocbuild/bbs-3.15-bioc/R/library/RNAdecay/libs/x64/general_Exp_4sse.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'F:/biocbuild/bbs-3.15-bioc/R/library/RNAdecay/libs/x64/general_dExp_1sse.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'F:/biocbuild/bbs-3.15-bioc/R/library/RNAdecay/libs/x64/general_dExp_2sse.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'F:/biocbuild/bbs-3.15-bioc/R/library/RNAdecay/libs/x64/general_dExp_3sse.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'F:/biocbuild/bbs-3.15-bioc/R/library/RNAdecay/libs/x64/general_dExp_4sse.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'F:/biocbuild/bbs-3.15-bioc/meat/RNAdecay.Rcheck/00check.log'
for details.
RNAdecay.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL RNAdecay
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'RNAdecay' ...
** using staged installation
** libs
running 'src/Makefile.win' ...
F:/biocbuild/bbs-3.15-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)"
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"F:/biocbuild/bbs-3.15-bioc/R/library/TMB/include" -I"F:/biocbuild/bbs-3.15-bioc/R/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_dExp_1sse -DCPPAD_FRAMEWORK -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c general_dExp_1sse.cpp -o general_dExp_1sse.o
g++ -std=gnu++11 -shared -s -static-libgcc -o general_dExp_1sse.dll tmp.def general_dExp_1sse.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
[1] 0
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.4.1
Current Matrix version is 1.5.1
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
F:/biocbuild/bbs-3.15-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)"
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"F:/biocbuild/bbs-3.15-bioc/R/library/TMB/include" -I"F:/biocbuild/bbs-3.15-bioc/R/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_Exp_1sse -DCPPAD_FRAMEWORK -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c general_Exp_1sse.cpp -o general_Exp_1sse.o
g++ -std=gnu++11 -shared -s -static-libgcc -o general_Exp_1sse.dll tmp.def general_Exp_1sse.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
[1] 0
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.4.1
Current Matrix version is 1.5.1
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
F:/biocbuild/bbs-3.15-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)"
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"F:/biocbuild/bbs-3.15-bioc/R/library/TMB/include" -I"F:/biocbuild/bbs-3.15-bioc/R/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_dExp_2sse -DCPPAD_FRAMEWORK -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c general_dExp_2sse.cpp -o general_dExp_2sse.o
g++ -std=gnu++11 -shared -s -static-libgcc -o general_dExp_2sse.dll tmp.def general_dExp_2sse.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
[1] 0
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.4.1
Current Matrix version is 1.5.1
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
F:/biocbuild/bbs-3.15-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)"
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"F:/biocbuild/bbs-3.15-bioc/R/library/TMB/include" -I"F:/biocbuild/bbs-3.15-bioc/R/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_Exp_2sse -DCPPAD_FRAMEWORK -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c general_Exp_2sse.cpp -o general_Exp_2sse.o
g++ -std=gnu++11 -shared -s -static-libgcc -o general_Exp_2sse.dll tmp.def general_Exp_2sse.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
[1] 0
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.4.1
Current Matrix version is 1.5.1
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
F:/biocbuild/bbs-3.15-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)"
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"F:/biocbuild/bbs-3.15-bioc/R/library/TMB/include" -I"F:/biocbuild/bbs-3.15-bioc/R/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_dExp_3sse -DCPPAD_FRAMEWORK -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c general_dExp_3sse.cpp -o general_dExp_3sse.o
g++ -std=gnu++11 -shared -s -static-libgcc -o general_dExp_3sse.dll tmp.def general_dExp_3sse.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
[1] 0
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.4.1
Current Matrix version is 1.5.1
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
F:/biocbuild/bbs-3.15-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)"
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"F:/biocbuild/bbs-3.15-bioc/R/library/TMB/include" -I"F:/biocbuild/bbs-3.15-bioc/R/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_Exp_3sse -DCPPAD_FRAMEWORK -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c general_Exp_3sse.cpp -o general_Exp_3sse.o
g++ -std=gnu++11 -shared -s -static-libgcc -o general_Exp_3sse.dll tmp.def general_Exp_3sse.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
[1] 0
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.4.1
Current Matrix version is 1.5.1
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
F:/biocbuild/bbs-3.15-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)"
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"F:/biocbuild/bbs-3.15-bioc/R/library/TMB/include" -I"F:/biocbuild/bbs-3.15-bioc/R/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_dExp_4sse -DCPPAD_FRAMEWORK -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c general_dExp_4sse.cpp -o general_dExp_4sse.o
g++ -std=gnu++11 -shared -s -static-libgcc -o general_dExp_4sse.dll tmp.def general_dExp_4sse.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
[1] 0
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.4.1
Current Matrix version is 1.5.1
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
F:/biocbuild/bbs-3.15-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)"
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"F:/biocbuild/bbs-3.15-bioc/R/library/TMB/include" -I"F:/biocbuild/bbs-3.15-bioc/R/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_Exp_4sse -DCPPAD_FRAMEWORK -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c general_Exp_4sse.cpp -o general_Exp_4sse.o
g++ -std=gnu++11 -shared -s -static-libgcc -o general_Exp_4sse.dll tmp.def general_Exp_4sse.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
[1] 0
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.4.1
Current Matrix version is 1.5.1
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 F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-RNAdecay/00new/RNAdecay/libs/x64
** 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
** 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 | 0 | 0 | |
| aic | 0 | 0 | 0 | |
| cols | 0 | 0 | 0 | |
| comb_cv | 0 | 0 | 0 | |
| const_decay | 0 | 0 | 0 | |
| constraint_fun_list_maker | 0 | 0 | 0 | |
| decay_plot | 1.06 | 0.06 | 1.13 | |
| fit_var | 0 | 0 | 0 | |
| group_map | 0.08 | 0.02 | 0.10 | |
| groupings | 0 | 0 | 0 | |
| hl_plot | 1 | 0 | 1 | |
| log_lik | 0 | 0 | 0 | |
| mod_optimization | 1.58 | 0.06 | 1.79 | |
| n_par | 0 | 0 | 0 | |
| plain_theme | 0.08 | 0.01 | 0.10 | |
| sse_null_decaying_decay | 0 | 0 | 0 | |