Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Tue, 28 Apr 2020 10:56:20 -0700

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 <hpa...@fredhutch.org>
Sent: Tuesday, April 28, 2020 10:32 AM
To: Charles Warden <cwar...@coh.org>; Shepherd, Lori <lori.sheph...@roswellpark.org>; 
'bioc-devel@r-project.org' <bioc-devel@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.sheph...@roswellpark.org>
*Sent:* Tuesday, April 28, 2020 5:29 AM
*To:* Charles Warden <cwar...@coh.org>; Hervé Pagès
<hpa...@fredhutch.org>; 'bioc-devel@r-project.org'
<bioc-devel@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 <cwar...@coh.org <mailto:cwar...@coh.org>>
*Sent:* Monday, April 27, 2020 12:27 PM
*To:* Hervé Pagès <hpa...@fredhutch.org
<mailto:hpa...@fredhutch.org>>; Shepherd, Lori
<lori.sheph...@roswellpark.org <mailto:lori.sheph...@roswellpark.org>>; 
'bioc-devel@r-project.org'
<bioc-devel@r-project.org <mailto:bioc-devel@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@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 <hpa...@fredhutch.org <mailto:hpa...@fredhutch.org>>
Sent: Thursday, April 23, 2020 12:23 PM
To: Charles Warden <cwar...@coh.org <mailto:cwar...@coh.org>>;
Shepherd, Lori <lori.sheph...@roswellpark.org
<mailto:lori.sheph...@roswellpark.org>>; 'bioc-devel@r-project.org'
<bioc-devel@r-project.org <mailto:bioc-devel@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: hpa...@fredhutch.org <mailto:hpa...@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.



--
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: hpa...@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: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel























					Reply via email to