[Bioc-devel] Windows Development Build Error Message for COHCAP
Charles Warden
cw@rden @end|ng |rom coh@org
Tue Apr 28 18:02:12 CEST 2020
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://www.bioconductor.org/packages/release/bioc/html/COHCAP.html
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/placeholders.hpp:24,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/apply.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/contains.hpp:20,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/policies/policy.hpp:10,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/special_functions/beta.hpp:13,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/distributions/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/placeholders.hpp:24,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/apply.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/contains.hpp:20,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/policies/policy.hpp:10,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/special_functions/beta.hpp:13,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/distributions/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/placeholders.hpp:24,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/apply.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/contains.hpp:20,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/policies/policy.hpp:10,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/special_functions/beta.hpp:13,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/distributions/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/COHCAP/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://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<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/placeholders.hpp:24,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/apply.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/contains.hpp:20,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/policies/policy.hpp:10,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/special_functions/beta.hpp:13,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/distributions/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/placeholders.hpp:24,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/apply.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/contains.hpp:20,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/policies/policy.hpp:10,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/special_functions/beta.hpp:13,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/distributions/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/placeholders.hpp:24,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/mpl/apply.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/contains.hpp:20,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/policies/policy.hpp:10,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/special_functions/beta.hpp:13,
from C:/Users/Charles/Documents/R/win-library/4.0/BH/include/boost/math/distributions/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/COHCAP/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 information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301)
------------------------------------------------------------
This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]
More information about the Bioc-devel
mailing list