Reed Sorenson
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/RNAdecay |
| git_branch: devel |
| git_last_commit: 42841c3 |
| git_last_commit_date: 2024-10-29 11:26:41 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:42 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 1756/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RNAdecay 1.27.0 (landing page) Reed Sorenson
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 1.27.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RNAdecay.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings RNAdecay_1.27.0.tar.gz |
| StartedAt: 2024-12-24 04:21:21 -0500 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 04:23:42 -0500 (Tue, 24 Dec 2024) |
| EllapsedTime: 141.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RNAdecay.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RNAdecay.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings RNAdecay_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/RNAdecay.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RNAdecay/DESCRIPTION' ... OK
* this is package 'RNAdecay' version '1.27.0'
* 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
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* checking installed package size ... INFO
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 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/RNAdecay/libs/x64/general_Exp_1sse.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'E:/biocbuild/bbs-3.21-bioc/R/library/RNAdecay/libs/x64/general_Exp_2sse.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'E:/biocbuild/bbs-3.21-bioc/R/library/RNAdecay/libs/x64/general_Exp_3sse.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'E:/biocbuild/bbs-3.21-bioc/R/library/RNAdecay/libs/x64/general_Exp_4sse.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'E:/biocbuild/bbs-3.21-bioc/R/library/RNAdecay/libs/x64/general_dExp_1sse.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'E:/biocbuild/bbs-3.21-bioc/R/library/RNAdecay/libs/x64/general_dExp_2sse.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'E:/biocbuild/bbs-3.21-bioc/R/library/RNAdecay/libs/x64/general_dExp_3sse.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
File 'E:/biocbuild/bbs-3.21-bioc/R/library/RNAdecay/libs/x64/general_dExp_4sse.dll':
Found '_exit', possibly from '_exit' (C)
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 nor [v]sprintf. 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 ... 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
'E:/biocbuild/bbs-3.21-bioc/meat/RNAdecay.Rcheck/00check.log'
for details.
RNAdecay.Rcheck/00install.out
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###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL RNAdecay
###
##############################################################################
##############################################################################
* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'RNAdecay' ...
** using staged installation
** libs
running 'src/Makefile.win' ...
E:/biocbuild/bbs-3.21-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"E:/biocbuild/bbs-3.21-bioc/R/library/TMB/include" -I"E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_dExp_1sse -DCPPAD_FRAMEWORK -I"C:/rtools44/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++17 -shared -s -static-libgcc -o general_dExp_1sse.dll tmp.def general_dExp_1sse.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
[1] 0
E:/biocbuild/bbs-3.21-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_1sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"E:/biocbuild/bbs-3.21-bioc/R/library/TMB/include" -I"E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_Exp_1sse -DCPPAD_FRAMEWORK -I"C:/rtools44/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++17 -shared -s -static-libgcc -o general_Exp_1sse.dll tmp.def general_Exp_1sse.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
[1] 0
E:/biocbuild/bbs-3.21-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"E:/biocbuild/bbs-3.21-bioc/R/library/TMB/include" -I"E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_dExp_2sse -DCPPAD_FRAMEWORK -I"C:/rtools44/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++17 -shared -s -static-libgcc -o general_dExp_2sse.dll tmp.def general_dExp_2sse.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
[1] 0
E:/biocbuild/bbs-3.21-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_2sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"E:/biocbuild/bbs-3.21-bioc/R/library/TMB/include" -I"E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_Exp_2sse -DCPPAD_FRAMEWORK -I"C:/rtools44/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++17 -shared -s -static-libgcc -o general_Exp_2sse.dll tmp.def general_Exp_2sse.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
[1] 0
E:/biocbuild/bbs-3.21-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"E:/biocbuild/bbs-3.21-bioc/R/library/TMB/include" -I"E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_dExp_3sse -DCPPAD_FRAMEWORK -I"C:/rtools44/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++17 -shared -s -static-libgcc -o general_dExp_3sse.dll tmp.def general_dExp_3sse.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
[1] 0
E:/biocbuild/bbs-3.21-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_3sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"E:/biocbuild/bbs-3.21-bioc/R/library/TMB/include" -I"E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_Exp_3sse -DCPPAD_FRAMEWORK -I"C:/rtools44/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++17 -shared -s -static-libgcc -o general_Exp_3sse.dll tmp.def general_Exp_3sse.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
[1] 0
E:/biocbuild/bbs-3.21-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_dExp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"E:/biocbuild/bbs-3.21-bioc/R/library/TMB/include" -I"E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_dExp_4sse -DCPPAD_FRAMEWORK -I"C:/rtools44/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++17 -shared -s -static-libgcc -o general_dExp_4sse.dll tmp.def general_dExp_4sse.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
[1] 0
E:/biocbuild/bbs-3.21-bioc/R/bin/Rscript --vanilla -e "TMB::compile('general_Exp_4sse.cpp',safebounds=FALSE,safeunload=FALSE)"
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I"E:/biocbuild/bbs-3.21-bioc/R/library/TMB/include" -I"E:/biocbuild/bbs-3.21-bioc/R/library/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_general_Exp_4sse -DCPPAD_FRAMEWORK -I"C:/rtools44/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++17 -shared -s -static-libgcc -o general_Exp_4sse.dll tmp.def general_Exp_4sse.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
[1] 0
installing to E:/biocbuild/bbs-3.21-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 | 0.01 | 0.00 | 0.02 | |
| comb_cv | 0 | 0 | 0 | |
| const_decay | 0 | 0 | 0 | |
| constraint_fun_list_maker | 0 | 0 | 0 | |
| decay_plot | 1.13 | 0.08 | 1.20 | |
| fit_var | 0 | 0 | 0 | |
| group_map | 0.07 | 0.03 | 0.11 | |
| groupings | 0 | 0 | 0 | |
| hl_plot | 1.42 | 0.05 | 1.47 | |
| log_lik | 0 | 0 | 0 | |
| mod_optimization | 1.49 | 0.11 | 1.60 | |
| n_par | 0 | 0 | 0 | |
| plain_theme | 0.11 | 0.00 | 0.11 | |
| sse_null_decaying_decay | 0 | 0 | 0 | |