[Bioc-devel] Windows Development Build Error Message for COHCAP
Hervé Pagès
hp@ge@ @end|ng |rom |redhutch@org
Tue Apr 28 19:55:10 CEST 2020
It is not clear what the purpose of these "if" statement is. Apparently
to set the $os_name variable but then where is this variable used and
for what?
So you might want to revisit the need for these tests. Maybe you don't
need them after all.
Another problem is that the temporary files generated by your Perl
scripts are generated in the current working directory. As discussed
earlier, this is not good. Please make sure that all temporary files are
generated in tempdir().
Thanks!
H.
On 4/28/20 10:43, Charles Warden wrote:
> Hi H,
>
> Thank you for pointing that out.
>
> I am currently not seeing errors on my Windows computer, but I see that I need to add "msys" for Windows on your system (and add quotes as well as make the error message more clear). I have a 64-bit Windows computer and I didn't get an error message, but I can see how this could cause problems. I apologize for not realizing that.
>
> It sounds like I should wait a little while to do that. However, I think this does sound correct, and I will make that change.
>
> Thank You,
> Charles
>
> -----Original Message-----
> From: Hervé Pagès <hpages using fredhutch.org>
> Sent: Tuesday, April 28, 2020 10:32 AM
> To: Charles Warden <cwarden using coh.org>; Shepherd, Lori <Lori.Shepherd using RoswellPark.org>; 'bioc-devel using r-project.org' <bioc-devel using r-project.org>
> Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP
>
> Hi Charles,
>
> The error you get on Windows is because your Perl script integrate_island.pl fails on this platform. It contains the following code:
>
> if (($os eq "MacOS")||($os eq "darwin")||($os eq "linux"))
> {
> #Mac
> $os_name = "MAC";
> }#end if ($os eq "MacOS")
> elsif ($os eq "MSWin32")
> {
> #PC
> $os_name = "PC";
> }#end if ($os eq "MacOS")
> else
> {
> print "Need to specify folder structure for $os!\n";
> exit;
> }#end else
>
> The major problem with this code is that the script will exit
> **normally** without doing anything if the detected OS is not one of the expected ones. So the 'temp_paired_367853.txt' file is not produced and your R code later fails to open it (when you try to read the file with read.table()).
>
> Note that before exiting, your Perl script displays:
>
> Need to specify folder structure for msys!
>
> which you can see in the report. This gives you a BIG clue of what the problem is and how to fix it.
>
> If you develop your package on Windows (and it seems you do), the problem should be very reproducible for you, granted that you use R
> 4.0.0 for that of course.
>
> Thanks,
> H.
>
>
> On 4/28/20 09:02, Charles Warden wrote:
>> Hi Lori,
>>
>> Thank you very much.
>>
>> I was thinking about reverting the change to test not specifying the
>> full file path at one point (in *v1.33.6*), but I was planning on
>> keeping the change to using a temporary directory in *v1.33.4*.
>> Essentially, I tested making that change in *v1.33.6* because there
>> was still an error message in *v1.33.4.*
>>
>> However, I will wait to see what else you suggest, before making any
>> additional changes. From my end, there is no need to rush, and I can
>> wait until next week (or later).
>>
>> You probably already know this, but it looks like *v1.33.6 *is in the
>> release version without any errors (although it does look like the
>> Windows version is different):
>>
>> https://urldefense.com/v3/__https://www.bioconductor.org/packages/rele
>> ase/bioc/html/COHCAP.html__;!!Fou38LsQmgU!_wdP4PPRbzvocGetxQ4gXCipwd4_
>> 1cOH4l3X1xkG8DChTNm0z7KryGwjVxBW$
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.bioconductor
>> .org_packages_release_bioc_html_COHCAP.html&d=DwMGaQ&c=eRAMFD45gAfqt84
>> VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=OANP0q_4ipib1q
>> 0Y0KadeY9Api_-E4mZFZDodVQ8gMY&s=9TOVgc79RcLRStlZDJLBYL-wmdRF4rBN6aWrEG
>> gHdGQ&e=>
>>
>> So, if I understand everything, I think this is OK.
>>
>> Thanks Again,
>>
>> Charles
>>
>> *From:*Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
>> *Sent:* Tuesday, April 28, 2020 5:29 AM
>> *To:* Charles Warden <cwarden using coh.org>; Hervé Pagès
>> <hpages using fredhutch.org>; 'bioc-devel using r-project.org'
>> <bioc-devel using r-project.org>
>> *Subject:* Re: [Bioc-devel] Windows Development Build Error Message
>> for COHCAP
>>
>> I can investigate more on the windows machine after we are done with
>> the release (later this week -- possibly early next)
>>
>> I would highly recommend not reverting the change to using a
>> temporary directory. We don't normally allow anyone to write to
>> anywhere but a temporary directory except in extreme circumstances.
>> New packages that are reviewed would not get accepted in Bioconductor if they did this.
>>
>> We appreciate your effort on trying to debug this and will help you
>> shortly.
>>
>> Cheers,
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Comprehensive Cancer Center
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>>
>> ----------------------------------------------------------------------
>> --
>>
>> *From:*Charles Warden <cwarden using coh.org <mailto:cwarden using coh.org>>
>> *Sent:* Monday, April 27, 2020 12:27 PM
>> *To:* Hervé Pagès <hpages using fredhutch.org
>> <mailto:hpages using fredhutch.org>>; Shepherd, Lori
>> <Lori.Shepherd using RoswellPark.org <mailto:Lori.Shepherd using RoswellPark.org>>; 'bioc-devel using r-project.org'
>> <bioc-devel using r-project.org <mailto:bioc-devel using r-project.org>>
>> *Subject:* RE: [Bioc-devel] Windows Development Build Error Message
>> for COHCAP
>>
>> Hi,
>>
>> I am not sure if I am going to have to wait to submit extra revisions.
>> However, I am unfortunately having the same issue (even though I
>> tested using the temporary directory instead of the current working
>> directory, in COHCAP (v.1.33.4).
>>
>> I also tested changing the file path to the temporary in v.1.33.6, but
>> that also didn't fix the problem (and I might change that back).
>>
>> I am also still not able to reproduce this error message on my end.
>>
>> For example, this is what the output of the build command looks like:
>>
>> C:\Users\Charles\Documents>"C:\Program Files\R\R-4.0.0\bin\R.exe" CMD
>> build COHCAP
>> * checking for file 'COHCAP/DESCRIPTION' ... OK
>> * preparing 'COHCAP':
>> * checking DESCRIPTION meta-information ... OK
>> * cleaning src
>> * installing the package to build vignettes
>> * creating vignettes ... OK
>> * cleaning src
>> * checking for LF line-endings in source and make files and shell
>> scripts
>> * checking for empty or unneeded directories
>> * building 'COHCAP_1.33.6.tar.gz'
>>
>> And, I can also install COHCAP successfully using devtools (in
>> R-4.0.0), although it does have some warnings:
>>
>>> library("devtools")
>> Loading required package: usethis
>>> devtools::install_github("cwarden45/COHCAP")
>> Skipping install of 'COHCAP' from a github remote, the SHA1 (09b017ba)
>> has not changed since last install.
>> Use `force = TRUE` to force installation
>>> devtools::install_github("cwarden45/COHCAP", force=TRUE)
>> Downloading GitHub repo cwarden45/COHCAP using master
>>
>>
>>
>> checking for file
>> 'C:\Users\Charles\AppData\Local\Temp\RtmpOIc4WV\remotes370c11a9aa0\cwarden45-COHCAP-09b017b/DESCRIPTION'
>> ...
>>
>> checking for file
>> 'C:\Users\Charles\AppData\Local\Temp\RtmpOIc4WV\remotes370c11a9aa0\cwarden45-COHCAP-09b017b/DESCRIPTION'
>> ...
>>
>> √ checking for file
>> 'C:\Users\Charles\AppData\Local\Temp\RtmpOIc4WV\remotes370c11a9aa0\cwarden45-COHCAP-09b017b/DESCRIPTION'
>> (339ms)
>>
>>
>>
>>
>> - preparing 'COHCAP':
>> checking DESCRIPTION meta-information ...
>>
>> checking DESCRIPTION meta-information ...
>>
>> √ checking DESCRIPTION meta-information
>> - cleaning src
>>
>>
>>
>>
>> - checking for LF line-endings in source and make files and shell
>> scripts
>>
>>
>>
>>
>> - checking for empty or unneeded directories
>>
>>
>>
>>
>> - building 'COHCAP_1.33.6.tar.gz'
>>
>>
>>
>>
>> Installing package into ‘C:/Users/Charles/Documents/R/win-library/4.0’
>> (as ‘lib’ is unspecified)
>> * installing *source* package 'COHCAP' ...
>> ** using staged installation
>> ** libs
>> "C:/rtools40/mingw64/bin/"g++ -std=gnu++11
>> -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG
>> -I'C:/Users/Charles/Documents/R/win-library/4.0/Rcpp/include'
>> -I'C:/Users/Charles/Documents/R/win-library/4.0/BH/include' -O2
>> -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o
>> RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11
>> -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG
>> -I'C:/Users/Charles/Documents/R/win-library/4.0/Rcpp/include'
>> -I'C:/Users/Charles/Documents/R/win-library/4.0/BH/include' -O2
>> -Wall -mfpmath=sse -msse2 -mstackrealign -c Rcpp_BH_ANOVA.cpp -o
>> Rcpp_BH_ANOVA.o In file included from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /na_assert.hpp:23,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/arg.
>> hpp:25,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/plac
>> eholders.hpp:24,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/appl
>> y.hpp:24,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /iter_apply.hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /find_if_pred.hpp:14,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/find
>> _if.hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/find
>> .hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /contains_impl.hpp:20,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/cont
>> ains.hpp:20,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/pol
>> icies/policy.hpp:10,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/spe
>> cial_functions/math_fwd.hpp:29,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/spe
>> cial_functions/beta.hpp:13,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/dis
>> tributions/fisher_f.hpp:12,
>> from Rcpp_BH_ANOVA.cpp:4:
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/assert.hpp:194:21:
>> warning: unnecessary parentheses in declaration of 'assert_arg'
>> [-Wparentheses]
>> failed ************ (Pred::************
>> ^
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/assert.hpp:199:21:
>> warning: unnecessary parentheses in declaration of 'assert_not_arg'
>> [-Wparentheses]
>> failed ************ (boost::mpl::not_<Pred>::************
>> ^
>> "C:/rtools40/mingw64/bin/"g++ -std=gnu++11
>> -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG
>> -I'C:/Users/Charles/Documents/R/win-library/4.0/Rcpp/include'
>> -I'C:/Users/Charles/Documents/R/win-library/4.0/BH/include' -O2
>> -Wall -mfpmath=sse -msse2 -mstackrealign -c
>> Rcpp_BH_linear_regression.cpp -o Rcpp_BH_linear_regression.o In file
>> included from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /na_assert.hpp:23,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/arg.
>> hpp:25,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/plac
>> eholders.hpp:24,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/appl
>> y.hpp:24,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /iter_apply.hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /find_if_pred.hpp:14,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/find
>> _if.hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/find
>> .hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /contains_impl.hpp:20,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/cont
>> ains.hpp:20,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/pol
>> icies/policy.hpp:10,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/spe
>> cial_functions/math_fwd.hpp:29,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/spe
>> cial_functions/beta.hpp:13,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/dis
>> tributions/students_t.hpp:16,
>> from Rcpp_BH_linear_regression.cpp:4:
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/assert.hpp:194:21:
>> warning: unnecessary parentheses in declaration of 'assert_arg'
>> [-Wparentheses]
>> failed ************ (Pred::************
>> ^
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/assert.hpp:199:21:
>> warning: unnecessary parentheses in declaration of 'assert_not_arg'
>> [-Wparentheses]
>> failed ************ (boost::mpl::not_<Pred>::************
>> ^
>> "C:/rtools40/mingw64/bin/"g++ -std=gnu++11
>> -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG
>> -I'C:/Users/Charles/Documents/R/win-library/4.0/Rcpp/include'
>> -I'C:/Users/Charles/Documents/R/win-library/4.0/BH/include' -O2
>> -Wall -mfpmath=sse -msse2 -mstackrealign -c Rcpp_BH_ttest.cpp -o
>> Rcpp_BH_ttest.o In file included from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /na_assert.hpp:23,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/arg.
>> hpp:25,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/plac
>> eholders.hpp:24,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/appl
>> y.hpp:24,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /iter_apply.hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /find_if_pred.hpp:14,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/find
>> _if.hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/find
>> .hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /contains_impl.hpp:20,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/cont
>> ains.hpp:20,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/pol
>> icies/policy.hpp:10,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/spe
>> cial_functions/math_fwd.hpp:29,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/spe
>> cial_functions/beta.hpp:13,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/dis
>> tributions/students_t.hpp:16,
>> from Rcpp_BH_ttest.cpp:4:
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/assert.hpp:194:21:
>> warning: unnecessary parentheses in declaration of 'assert_arg'
>> [-Wparentheses]
>> failed ************ (Pred::************
>> ^
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/assert.hpp:199:21:
>> warning: unnecessary parentheses in declaration of 'assert_not_arg'
>> [-Wparentheses]
>> failed ************ (boost::mpl::not_<Pred>::************
>> ^
>> C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o
>> COHCAP.dll tmp.def RcppExports.o Rcpp_BH_ANOVA.o
>> Rcpp_BH_linear_regression.o Rcpp_BH_ttest.o
>> -LC:/PROGRA~1/R/R-40~1.0/bin/x64 -lR
>> installing to
>> C:/Users/Charles/Documents/R/win-library/4.0/00LOCK-COHCAP/00new/COHCA
>> P/libs/x64
>> ** R
>> ** inst
>> ** byte-compile and prepare package for lazy loading
>> ** help
>> *** installing help indices
>> converting help for package 'COHCAP'
>> finding HTML links ... done
>> COHCAP.BSSeq.preprocess html
>> COHCAP.BSSeq_V2.methyl.table html
>> COHCAP.annotate html
>> COHCAP.avg.by.island html
>> COHCAP.avg.by.site html
>> COHCAP.denovo html
>> COHCAP.integrate.avg.by.island html
>> COHCAP.integrate.avg.by.site html
>> COHCAP.qc html
>> COHCAP.reformatFinalReport html
>> COHCAP.site html
>> ** 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 (COHCAP)
>>
>> If I try to install COHCAP using the Bioconductor commands (in
>> R-4.0.0), then I get a general warning message before being able to
>> install COHCAP (but the installation does otherwise run to completion):
>>
>>> if (!requireNamespace("BiocManager", quietly = TRUE))
>> + install.packages("BiocManager")
>>> BiocManager::install(version='devel')
>> Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
>> Installation path not writeable, unable to update packages: boot,
>> class,
>> foreign, KernSmooth, MASS, nnet, spatial
>>> BiocManager::install("COHCAP")
>> Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
>> Installing package(s) 'COHCAP'
>>
>> There is a binary version available but the source version is later:
>> binary source needs_compilation COHCAP 1.33.1 1.33.4
>> TRUE
>>
>> installing the source package ‘COHCAP’
>>
>> trying URL
>> 'https://urldefense.com/v3/__https://secure-web.cisco.com/1p0sXL52SsCl
>> hOHNiIzZww4J8w03mGvAE35d40loIi_OhURYl2_aIoQHiz-vxMtio-tYkY3zDgYUrKDGUg
>> Fn9wnCsFXA0DRgqyKoc-OxCZuUXdY9Jlf9njf1CzojyMvVEK5rbCMpJ1sGq9rTt-6aFVqC
>> gGXHVJH9MpQ5VXJLpfi_pWe4ik7pP0aEalNQmePfzN4ddEz4dRQik26E3PsuA3aWt0MDYY
>> fi2qjx9jvz8IUwxqFi_zoST75afYxnHb1-CBKWegOQ9TklAwYcxrJDBdDIhAvVl3gBX5Ix
>> D_SNm0VNrjM89hv-zJCOKDXNPzoGjBS__x4abB5EoU2DxpVDPvgqCCu2tUUTehZC3EcY6e
>> l4/https*3A*2F*2Fbioconductor.org*2Fpackages*2F3.11*2Fbioc*2Fsrc*2Fcon
>> trib*2FCOHCAP_1.33.4.tar.gz__;JSUlJSUlJSUl!!Fou38LsQmgU!_wdP4PPRbzvocG
>> etxQ4gXCipwd4_1cOH4l3X1xkG8DChTNm0z7KryBdMkmOn$
>> <https://urldefense.com/v3/__https:/secure-web.cisco.com/1p0sXL52SsClhOHNiIzZww4J8w03mGvAE35d40loIi_OhURYl2_aIoQHiz-vxMtio-tYkY3zDgYUrKDGUgFn9wnCsFXA0DRgqyKoc-OxCZuUXdY9Jlf9njf1CzojyMvVEK5rbCMpJ1sGq9rTt-6aFVqCgGXHVJH9MpQ5VXJLpfi_pWe4ik7pP0aEalNQmePfzN4ddEz4dRQik26E3PsuA3aWt0MDYYfi2qjx9jvz8IUwxqFi_zoST75afYxnHb1-CBKWegOQ9TklAwYcxrJDBdDIhAvVl3gBX5IxD_SNm0VNrjM89hv-zJCOKDXNPzoGjBS__x4abB5EoU2DxpVDPvgqCCu2tUUTehZC3EcY6el4/https*3A*2F*2Fbioconductor.org*2Fpackages*2F3.11*2Fbioc*2Fsrc*2Fcontrib*2FCOHCAP_1.33.4.tar.gz__;JSUlJSUlJSUl!!Fou38LsQmgU!_CA9vAtCM3BDn308oMt6D3dTByhTBxuQoOyvVDaIuZXdqT2gkgCSJkJR4JNH$>'
>> Content type 'application/x-gzip' length 194066 bytes (189 KB)
>> downloaded 189 KB
>>
>> * installing *source* package 'COHCAP' ...
>> ** using staged installation
>> ** libs
>> "C:/rtools40/mingw64/bin/"g++ -std=gnu++11
>> -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG
>> -I'C:/Users/Charles/Documents/R/win-library/4.0/Rcpp/include'
>> -I'C:/Users/Charles/Documents/R/win-library/4.0/BH/include' -O2
>> -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o
>> RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11
>> -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG
>> -I'C:/Users/Charles/Documents/R/win-library/4.0/Rcpp/include'
>> -I'C:/Users/Charles/Documents/R/win-library/4.0/BH/include' -O2
>> -Wall -mfpmath=sse -msse2 -mstackrealign -c Rcpp_BH_ANOVA.cpp -o
>> Rcpp_BH_ANOVA.o In file included from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /na_assert.hpp:23,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/arg.
>> hpp:25,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/plac
>> eholders.hpp:24,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/appl
>> y.hpp:24,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /iter_apply.hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /find_if_pred.hpp:14,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/find
>> _if.hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/find
>> .hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /contains_impl.hpp:20,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/cont
>> ains.hpp:20,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/pol
>> icies/policy.hpp:10,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/spe
>> cial_functions/math_fwd.hpp:29,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/spe
>> cial_functions/beta.hpp:13,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/dis
>> tributions/fisher_f.hpp:12,
>> from Rcpp_BH_ANOVA.cpp:4:
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/assert.hpp:194:21:
>> warning: unnecessary parentheses in declaration of 'assert_arg'
>> [-Wparentheses]
>> failed ************ (Pred::************
>> ^
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/assert.hpp:199:21:
>> warning: unnecessary parentheses in declaration of 'assert_not_arg'
>> [-Wparentheses]
>> failed ************ (boost::mpl::not_<Pred>::************
>> ^
>> "C:/rtools40/mingw64/bin/"g++ -std=gnu++11
>> -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG
>> -I'C:/Users/Charles/Documents/R/win-library/4.0/Rcpp/include'
>> -I'C:/Users/Charles/Documents/R/win-library/4.0/BH/include' -O2
>> -Wall -mfpmath=sse -msse2 -mstackrealign -c
>> Rcpp_BH_linear_regression.cpp -o Rcpp_BH_linear_regression.o In file
>> included from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /na_assert.hpp:23,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/arg.
>> hpp:25,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/plac
>> eholders.hpp:24,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/appl
>> y.hpp:24,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /iter_apply.hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /find_if_pred.hpp:14,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/find
>> _if.hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/find
>> .hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /contains_impl.hpp:20,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/cont
>> ains.hpp:20,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/pol
>> icies/policy.hpp:10,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/spe
>> cial_functions/math_fwd.hpp:29,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/spe
>> cial_functions/beta.hpp:13,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/dis
>> tributions/students_t.hpp:16,
>> from Rcpp_BH_linear_regression.cpp:4:
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/assert.hpp:194:21:
>> warning: unnecessary parentheses in declaration of 'assert_arg'
>> [-Wparentheses]
>> failed ************ (Pred::************
>> ^
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/assert.hpp:199:21:
>> warning: unnecessary parentheses in declaration of 'assert_not_arg'
>> [-Wparentheses]
>> failed ************ (boost::mpl::not_<Pred>::************
>> ^
>> "C:/rtools40/mingw64/bin/"g++ -std=gnu++11
>> -I"C:/PROGRA~1/R/R-40~1.0/include" -DNDEBUG
>> -I'C:/Users/Charles/Documents/R/win-library/4.0/Rcpp/include'
>> -I'C:/Users/Charles/Documents/R/win-library/4.0/BH/include' -O2
>> -Wall -mfpmath=sse -msse2 -mstackrealign -c Rcpp_BH_ttest.cpp -o
>> Rcpp_BH_ttest.o In file included from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /na_assert.hpp:23,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/arg.
>> hpp:25,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/plac
>> eholders.hpp:24,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/appl
>> y.hpp:24,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /iter_apply.hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /find_if_pred.hpp:14,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/find
>> _if.hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/find
>> .hpp:17,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/aux_
>> /contains_impl.hpp:20,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/cont
>> ains.hpp:20,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/pol
>> icies/policy.hpp:10,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/spe
>> cial_functions/math_fwd.hpp:29,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/spe
>> cial_functions/beta.hpp:13,
>> from
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/dis
>> tributions/students_t.hpp:16,
>> from Rcpp_BH_ttest.cpp:4:
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/assert.hpp:194:21:
>> warning: unnecessary parentheses in declaration of 'assert_arg'
>> [-Wparentheses]
>> failed ************ (Pred::************
>> ^
>> C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/assert.hpp:199:21:
>> warning: unnecessary parentheses in declaration of 'assert_not_arg'
>> [-Wparentheses]
>> failed ************ (boost::mpl::not_<Pred>::************
>> ^
>> C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o
>> COHCAP.dll tmp.def RcppExports.o Rcpp_BH_ANOVA.o
>> Rcpp_BH_linear_regression.o Rcpp_BH_ttest.o
>> -LC:/PROGRA~1/R/R-40~1.0/bin/x64 -lR
>> installing to
>> C:/Users/Charles/Documents/R/win-library/4.0/00LOCK-COHCAP/00new/COHCA
>> P/libs/x64
>> ** R
>> ** inst
>> ** byte-compile and prepare package for lazy loading
>> ** help
>> *** installing help indices
>> converting help for package 'COHCAP'
>> finding HTML links ... done
>> COHCAP.BSSeq.preprocess html
>> COHCAP.BSSeq_V2.methyl.table html
>> COHCAP.annotate html
>> COHCAP.avg.by.island html
>> COHCAP.avg.by.site html
>> COHCAP.denovo html
>> COHCAP.integrate.avg.by.island html
>> COHCAP.integrate.avg.by.site html
>> COHCAP.qc html
>> COHCAP.reformatFinalReport html
>> COHCAP.site html
>> ** 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 (COHCAP)
>>
>> The downloaded source packages are in
>> ‘C:\Users\Charles\AppData\Local\Temp\Rtmp88lsk0\downloaded_packages’
>> Installation path not writeable, unable to update packages: boot,
>> class,
>> foreign, KernSmooth, MASS, nnet, spatial
>>
>> I am not sure if this last warning about the installation path has
>> something to do with using both the pre-release (previously) and
>> release
>> (currently) versions of R-4.0.0.
>>
>> Can you please help me know if you have any other troubleshooting
>> suggestions for the Window server used to test the Bioconductor packages?
>>
>> Thank You,
>> Charles
>>
>> -----Original Message-----
>> From: Hervé Pagès <hpages using fredhutch.org <mailto:hpages using fredhutch.org>>
>> Sent: Thursday, April 23, 2020 12:23 PM
>> To: Charles Warden <cwarden using coh.org <mailto:cwarden using coh.org>>;
>> Shepherd, Lori <Lori.Shepherd using RoswellPark.org
>> <mailto:Lori.Shepherd using RoswellPark.org>>; 'bioc-devel using r-project.org'
>> <bioc-devel using r-project.org <mailto:bioc-devel using r-project.org>>
>> Subject: Re: [Bioc-devel] Windows Development Build Error Message for
>> COHCAP
>>
>> [Attention: This email came from an external source. Do not open
>> attachments or click on links from unknown senders or unexpected
>> emails.]
>>
>> ----------------------------------------------------------------------
>> Hi Charles,
>>
>> On 4/23/20 10:19, Charles Warden wrote:
>>
>>> My guess was that creating the temporary file in the working directory instead of another folder might help.
>>
>> FWIW here are 2 important reasons for writing temporary stuff to
>> tempdir() instead of the current working directory:
>>
>> 1. tempdir() is the only place that is guaranteed to be writable on
>> every system. Yes the user home is very likely to be writable too but
>> there is actually no guarantee and some systems have unconventional
>> setups where it's not.
>>
>> 2. Whatever you put in tempdir() will automatically be removed at the
>> end of the R session. Even though there are ways to achieve this with
>> the temporary stuff you write in the user home, it's not automatic and
>> hard to get right.
>>
>> Cheers,
>> H.
>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages using fredhutch.org <mailto:hpages using fredhutch.org>
>> Phone: (206) 667-5791
>> Fax: (206) 667-1319
>>
>> ----------------------------------------------------------------------
>> ------------------------------------------------------------
>> -SECURITY/CONFIDENTIALITY WARNING-
>>
>> This message and any attachments are intended solely for the
>> individual or entity to which they are addressed. This communication
>> may contain information that is privileged, confidential, or exempt
>> from disclosure under applicable law (e.g., personal health
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>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages using fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages using fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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