kasperdanielhansen
commented
1 year ago Fixed in version 1.71.2.
Closed HenrikBengtsson closed 1 year ago
kasperdanielhansen
commented
1 year ago Fixed in version 1.71.2.
HenrikBengtsson
commented
1 year ago Awesome. Thanks. Let's keep this open until it passes on Bioc devel.
HenrikBengtsson
commented
1 year ago Confirming this also fixed it on Bioc;
* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/affxparser.Rcheck'
* using R version 4.3.0 RC (2023-04-18 r84287 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'affxparser/DESCRIPTION' ... OK
* this is package 'affxparser' version '1.71.2'
* 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 'affxparser' can be installed ... WARNING
Found the following significant warnings:
fusion/file/TsvFile/TsvFile.cpp:4921:20: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
fusion/file/TsvFile/TsvFile.cpp:4970:20: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
fusion/util/AffxConv.cpp:124:15: warning: self-comparison always evaluates to false [-Wtautological-compare]
See 'F:/biocbuild/bbs-3.18-bioc/meat/affxparser.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... OK
* checking package 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 shell scripts ... 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-3.18-bioc/R/library/affxparser/libs/x64/affxparser.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'rand', possibly from 'rand' (C)
Found 'srand', possibly from 'srand' (C)
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 examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
readCdfDataFrame 1.93 0.15 7.94
readCdfNbrOfCellsPerUnitGroup 0.28 0.11 5.09
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'convertCel.R'
Running 'readCdfDataFrame.R'
Running 'readCdfQc.R'
Running 'readCdfUnitsWriteMap.R'
Running 'readCdfUnits_etal.R'
Running 'readCel.R'
Running 'readCelIntensities.R'
Running 'readCelRectangle.R'
Running 'readCelUnits.R'
Running 'readPgf.R'
Running 'testWriteAndReadEmptyCdf.R'
Running 'testWriteAndReadEmptyCel.R'
OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
'F:/biocbuild/bbs-3.18-bioc/meat/affxparser.Rcheck/00check.log'
for details.Like I said, I did not push from Github to Bioc, but did a "de-novo" editing. I don't know if synchronizing the two repos requires anything, but I suggest checking this now.
On Tue, Apr 25, 2023 at 2:30 PM Henrik Bengtsson @.***> wrote:
Closed #48 https://github.com/HenrikBengtsson/affxparser/issues/48 as completed.
— Reply to this email directly, view it on GitHub https://github.com/HenrikBengtsson/affxparser/issues/48#event-9095371386, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABF2DH65RLBUVCY65LDZ2C3XDAJ53ANCNFSM6AAAAAAWTDZ5BA . You are receiving this because you commented.Message ID: @.***>
-- Best, Kasper
Issue
Bioc devel reports installation errors on MS Windows (https://github.com/HenrikBengtsson/affxparser/actions/runs/4611292115/jobs/8150807388):
We can reproduce this on GitHub Actions (e.g. https://github.com/HenrikBengtsson/affxparser/actions/runs/4611292115/jobs/8150807388) using R-devel (to become R 4.4.0);