[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 at coh.org>
Sent: Monday, April 27, 2020 12:27 PM
To: Herv?? Pag??s <hpages at fredhutch.org>; Shepherd, Lori <Lori.Shepherd at RoswellPark.org>; 'bioc-devel at r-project.org' <bioc-devel at r-project.org>
Subject: RE: [Bioc-devel] Windows Development Build Error Message for COHCAP
Sent: Monday, April 27, 2020 12:27 PM
To: Herv?? Pag??s <hpages at fredhutch.org>; Shepherd, Lori <Lori.Shepherd at RoswellPark.org>; 'bioc-devel at r-project.org' <bioc-devel at 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 at 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'
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: Herv?? Pag??s <hpages at fredhutch.org>
Sent: Thursday, April 23, 2020 12:23 PM
To: Charles Warden <cwarden at coh.org>; Shepherd, Lori <Lori.Shepherd at RoswellPark.org>; 'bioc-devel at r-project.org' <bioc-devel at 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.]
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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.
--
Herv?? Pag??s
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 at fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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