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

12 messages · Charles Warden, Shepherd, Lori, Hervé Pagès

Original
Charles Warden
# 
Hi,

I noticed that I received a few error messages in the Windows build for COHCAP:

http://bioconductor.org/checkResults/devel/bioc-LATEST/COHCAP/tokay2-buildsrc.html

I changed the default settings to avoid an earlier error message (again, just on Windows), but I am currently getting an error message that I am having some trouble reproducing.

Can you help me with either of the following questions?


  1.  I apologize for the simple question, but where can I download the Windows executable for R-4.0.0?  I was able to reproduce and fix an earlier issue with R-devel (on Linux), but I was not certain how to get the error message for Windows.  I have tried to reproduce the error using the devtools installation from the GitHub code (https://github.com/cwarden45/COHCAP), but that can be installed successfully (with Windows R-3.6.3).
  2.  The .zip file for the Windows version on the devel page is different (http://bioconductor.org/packages/3.11/bioc/html/COHCAP.html), where I see cohcap_1.33.1.zip for Windows.  I think I saw the first error message in 1.33.1, and I made an intermediate change before changing the defaults to avoid the error message.  However, the strange thing was that I thought I saw an "OK" status while I was waiting for the 1.33.3 version to appear in the build reports (which I thought was for COHCAP 1.33.2).  Do all of the packages get re-built, regardless of whether an update is uploaded?
     *   I am wondering if there is a chance that I might be able to wait a day or two and see if I can get a status of "OK" for all steps on all of the test servers.  However, if that is true, then I am a little worried about what happens if there is a temporary error in the release version.


Thank you very much!

Sincerely,
Charles
Charles Warden, Bioinformatics Specialist
Integrative Genomics Core
City of Hope National Medical Center
Shamrock Monrovia Building (655 Huntington Dr, Monrovia, CA, 91016)
Room 1086
Internal Ext: 80375 | Direct: 626-218-0375

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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)
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Shepherd, Lori
# 
Thank you for your inquiry

R 4.0.0 can be downloaed from the following page. This patched page exists a few weeks out from the official R release for the patched version of R windows:


https://cran.r-project.org/bin/windows/base/rpatched.html


2.  Landing pages can have different versions of the file for different platforms when a package will build cleanly for one platform but not another.  We only propagate and make available successfully built packages.


3.  You can wait a day or two if you like but realize the 3.11 release is fast approaching.  If this stay ERROR and it is not fixed by monday you will have to push fixes to both a release 3.11 and the new devel branch (master branch prepping for 3.12 in fall).


4.  I'll try and log on our windows builder later today to see if I can track down any additional information for you to help debug.  If I find anything I will contact you about it.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
Shepherd, Lori
# 
In your vignette you also use   `getwd()`  to define your output directory.  Please change this to use a temporary directory  `tempdir()`


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
Charles Warden
# 
Hi Lori,

Thank you very much.

Yes - I understand that there is an upcoming deadline.

If I install the version of R for Windows that you provided and I install Rtools from the following link (https://cran.r-project.org/bin/windows/Rtools/), then I can still successfully install the devel version of COHCAP.

I can also use the regular Bioconductor installer to install the devel version of COHCAP on R-devel.

My guess was that creating the temporary file in the working directory instead of another folder might help.  However, since I am not getting an error message on my computer, it is a little hard to say for certain.  This also sounds somewhat similar to the change that you recommended.

So, I will make the change that you described (setting the output folder the temporary directory, using tempdir()), and see if that gets rid of the error message.  If not, I will continue to troubleshoot (but it sounds like that may require continuing to push updates after the deadline).

Thanks again!

Sincerely,
Charles

From: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
Sent: Thursday, April 23, 2020 5:00 AM
To: Charles Warden <cwarden at coh.org>; 'bioc-devel at r-project.org' <bioc-devel at r-project.org>
Subject: Re: Windows Development Build Error Message for COHCAP

Thank you for your inquiry

R 4.0.0 can be downloaed from the following page. This patched page exists a few weeks out from the official R release for the patched version of R windows:


https://cran.r-project.org/bin/windows/base/rpatched.html<https://urldefense.com/v3/__https:/cran.r-project.org/bin/windows/base/rpatched.html__;!!Fou38LsQmgU!-4yYGm9SusI6BqIJRZNxpBfOemJVFMIcb81007SoLoKzPxlHIIyWD5uBoQIj$>


2.  Landing pages can have different versions of the file for different platforms when a package will build cleanly for one platform but not another.  We only propagate and make available successfully built packages.


3.  You can wait a day or two if you like but realize the 3.11 release is fast approaching.  If this stay ERROR and it is not fixed by monday you will have to push fixes to both a release 3.11 and the new devel branch (master branch prepping for 3.12 in fall).


4.  I'll try and log on our windows builder later today to see if I can track down any additional information for you to help debug.  If I find anything I will contact you about it.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
Hervé Pagès
# 
Hi Charles,
On 4/23/20 10:19, Charles Warden wrote:

            

      
      
      
    

        
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.

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Charles Warden
    

    

      
      #
    

  


  

      
Hi H,

Thank you for the additional information.

I have pushed the git updates using tempdir() instead of getwd().  It sounds like that will probably fix the problem, and I will check tomorrow.

Best Wishes,
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.]

----------------------------------------------------------------------
Hi Charles,

        
On 4/23/20 10:19, Charles Warden wrote:

        

            

      
      
      
    

        
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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------------------------------------------------------------
-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)
------------------------------------------------------------

  
  


  


      

    

    
3 days later

    

      
      

        


  

        

      Charles Warden
    

    

      
      #
    

  


  

      
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:

            

      
      
      
    

        
Loading required package: usethis

            

      
      
      
    

        
Skipping install of 'COHCAP' from a github remote, the SHA1 (09b017ba) has not changed since last install.
  Use `force = TRUE` to force installation

            

      
      
      
    

        
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):

            

      
      
      
    

        
+     install.packages("BiocManager")

            

      
      
      
    

        
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

            

      
      
      
    

        
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://bioconductor.org/packages/3.11/bioc/src/contrib/COHCAP_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.]

----------------------------------------------------------------------
Hi Charles,

        
On 4/23/20 10:19, Charles Warden wrote:

        

            

      
      
      
    

        
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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      Shepherd, Lori
    

    

      
      #
    

  


  

      
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

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Charles Warden
    

    

      
      #
    

  


  

      
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 at RoswellPark.org>
Sent: Tuesday, April 28, 2020 5:29 AM
To: Charles Warden <cwarden at coh.org>; Herv? Pag?s <hpages at fredhutch.org>; 'bioc-devel at r-project.org' <bioc-devel at 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

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Hervé Pagès
    

    

      
      #
    

  


  

      
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:

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Charles Warden
    

    

      
      #
    

  


  

      
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: Herv? Pag?s <hpages at fredhutch.org> 
Sent: Tuesday, April 28, 2020 10:32 AM
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

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:

            

      
      
      
    

        
--
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

  
  


  


      

    

    

      
      

        


  

        

      Hervé Pagès
    

    

      
      #
    

  


  

      
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: