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This page was generated on 2024-03-29 11:36:31 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 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 40/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alabaster.base 1.2.1  (landing page)
Aaron Lun
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/alabaster.base
git_branch: RELEASE_3_18
git_last_commit: 7c9c73a
git_last_commit_date: 2023-11-06 10:45:23 -0400 (Mon, 06 Nov 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for alabaster.base on palomino4


To the developers/maintainers of the alabaster.base package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/alabaster.base.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: alabaster.base
Version: 1.2.1
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:alabaster.base.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings alabaster.base_1.2.1.tar.gz
StartedAt: 2024-03-27 22:15:51 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 22:18:22 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 150.7 seconds
RetCode: 0
Status:   OK  
CheckDir: alabaster.base.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:alabaster.base.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings alabaster.base_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/alabaster.base.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'alabaster.base/DESCRIPTION' ... OK
* this is package 'alabaster.base' version '1.2.1'
* 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 'alabaster.base' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
* 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 ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.18-bioc/R/library/alabaster.base/libs/x64/alabaster.base.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 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 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 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-3.18-bioc/meat/alabaster.base.Rcheck/00check.log'
for details.



Installation output

alabaster.base.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL alabaster.base
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'alabaster.base' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
using C++17
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c check_csv.cpp -o check_csv.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c check_df.cpp -o check_df.o
check_df.cpp: In function 'std::vector<takane::data_frame::ColumnDetails> configure_columns(Rcpp::CharacterVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::List)':
check_df.cpp:13:15: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
   13 |     if (ncols != column_types.size()) {
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~
check_df.cpp:16:15: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
   16 |     if (ncols != string_formats.size()) {
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
check_df.cpp:19:15: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
   19 |     if (ncols != factor_levels.size()) {
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c check_list.cpp -o check_list.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c load_csv.cpp -o load_csv.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c load_list.cpp -o load_list.o
g++  -std=gnu++17 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c write_scalar.cpp -o write_scalar.o
g++ -shared -s -static-libgcc -o alabaster.base.dll tmp.def RcppExports.o check_csv.o check_df.o check_list.o load_csv.o load_list.o write_scalar.o -LF:/biocbuild/bbs-3.18-bioc/R/library/Rhdf5lib/lib/x64-ucrt -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lsz -laec -lz -lpsapi -lz -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-alabaster.base/00new/alabaster.base/libs/x64
** R
** 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 (alabaster.base)

Tests output

alabaster.base.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(alabaster.base)
> test_check("alabaster.base")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 332 ]
> 
> proc.time()
   user  system elapsed 
  38.57    3.20   43.14 

Example timings

alabaster.base.Rcheck/alabaster.base-Ex.timings

nameusersystemelapsed
acquireFile0.410.040.44
altLoadObject0.270.000.26
altStageObject0.070.000.09
createRedirection0.320.020.30
listDirectory0.460.030.51
loadAtomicVector0.000.020.03
loadBaseFactor0.100.000.13
loadBaseList0.230.010.22
loadDataFrame0.110.000.12
loadDataFrameFactor0.280.020.33
loadDirectory0.460.000.52
loadObject0.070.010.09
moveObject0.550.030.58
quickLoadObject0.350.080.42
quickReadCsv0.060.000.06
removeObject0.440.020.41
saveFormats000
stageAtomicVector0.010.000.03
stageBaseFactor0.090.000.11
stageBaseList0.180.040.18
stageDataFrame0.030.040.08
stageDataFrameFactor0.240.000.23
stageObject0.050.000.06
transformVectorForHdf50.020.000.02
validateDirectory0.570.030.57
writeMetadata0.210.000.19