Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:26 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (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

CHECK results for Travel on palomino3


To the developers/maintainers of the Travel package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Travel.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.

raw results

Package 2045/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Travel 1.4.0  (landing page)
Jiefei Wang
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/Travel
git_branch: RELEASE_3_15
git_last_commit: afe6340
git_last_commit_date: 2022-04-26 12:12:45 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    TIMEOUT  skippedskipped

Summary

Package: Travel
Version: 1.4.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Travel.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Travel_1.4.0.tar.gz
StartedAt: 2022-10-19 04:55:53 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 04:57:43 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 110.1 seconds
RetCode: 0
Status:   OK  
CheckDir: Travel.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Travel.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Travel_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/Travel.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 'Travel/DESCRIPTION' ... OK
* this is package 'Travel' version '1.4.0'
* 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 'Travel' can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* 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-3.15-bioc/R/library/Travel/libs/x64/Travel.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 '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: 1 NOTE
See
  'F:/biocbuild/bbs-3.15-bioc/meat/Travel.Rcheck/00check.log'
for details.

Installation output

Travel.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Travel
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Travel' ...
** using staged installation
** libs
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Cpp_interface.cpp -o Cpp_interface.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c altfile_operations.cpp -o altfile_operations.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c altmmap_operations.cpp -o altmmap_operations.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c altrep_manager.cpp -o altrep_manager.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c class_Cache_block.cpp -o class_Cache_block.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c class_Filesystem_cache_copier.cpp -o class_Filesystem_cache_copier.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c class_Filesystem_file_data.cpp -o class_Filesystem_file_data.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c class_Memory_mapped.cpp -o class_Memory_mapped.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c class_Protect_guard.cpp -o class_Protect_guard.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c class_Subset_index.cpp -o class_Subset_index.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c class_Timer.cpp -o class_Timer.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c class_Unique_buffer.cpp -o class_Unique_buffer.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c examples.cpp -o examples.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c filesystem_manager.cpp -o filesystem_manager.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c filesystem_operations_dokan.cpp -o filesystem_operations_dokan.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c filesystem_operations_fuse.cpp -o filesystem_operations_fuse.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c memory_mapped_file.cpp -o memory_mapped_file.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c profile.cpp -o profile.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_write_operations.cpp -o read_write_operations.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c unit_test_utils.cpp -o unit_test_utils.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c unit_tests.cpp -o unit_tests.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:\Program Files\Dokan\Dokan Library-1.5.1\include" -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
g++ -shared -s -static-libgcc -o Travel.dll tmp.def Cpp_interface.o RcppExports.o altfile_operations.o altmmap_operations.o altrep_manager.o class_Cache_block.o class_Filesystem_cache_copier.o class_Filesystem_file_data.o class_Memory_mapped.o class_Protect_guard.o class_Subset_index.o class_Timer.o class_Unique_buffer.o examples.o filesystem_manager.o filesystem_operations_dokan.o filesystem_operations_fuse.o memory_mapped_file.o profile.o read_write_operations.o unit_test_utils.o unit_tests.o utils.o -LC:\Program Files\Dokan\Dokan Library-1.5.1\lib -ldokan1 -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
installing to F:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-Travel/00new/Travel/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 (Travel)

Tests output

Travel.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 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(Travel)
> 
> test_check("Travel")
The altmmap handle has been released: inode_12, handle: 0x00000218ba053970
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 156 ]
> 
> proc.time()
   user  system elapsed 
  41.90    1.68   51.12

Example timings

Travel.Rcheck/Travel-Ex.timings

nameusersystemelapsed
filesystem0.000.000.11
wrap_altrep000