Re: [Bioc-devel] Cairo error in Windows server

[Bunis, Daniel]

Thanks for these updates.

I get the same build error with my package, dittoSeq, so this can probably be 
"confirmed" as a 'Cairo installation issue that should clear up in tomorrow’s 
build reports' and not as an animalcules-specific issue.

Best,
Dan
___
Daniel Bunis
PhD Candidate, Burt & Sirota Labs
Biomedical Sciences Program
University of California, San Francisco
He/Him/His
daniel.bu...@ucsf.edu
856-905-0499

On Apr 14, 2020, at 12:10 PM, Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>> wrote:

I just reinstalled Cairo again to both architectures.  Cairo is known to be a 
particular challenging package for our builders.  It looks like a new version 
appeared on CRAN this past weekend.




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Yue Zhao (Jason) mailto:yu...@bu.edu>>
Sent: Monday, April 13, 2020 5:14 PM
To: Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>>
Cc: bioc-devel mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel] Cairo error in Windows server

Hi Lori,

Thanks for the previous update, but the same error shows up again today, would 
you please check the Cairo in the Windows server? Thank you!

PS. the error message: 
https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_animalcules_tokay1-2Dchecksrc.html=DwICAg=iORugZls2LlYyCAZRB3XLg=basuzE7-VlMupNUhjOlOjq3Z71OZ7WVlqjvCai9jtug=RxM38Ya7V3JXYe8RL_frUAtwMB3VxNvWT0XwWo3r1QY=yO7r-OhxEb5J3NpMF_FR94z00WX5uqyv-3rRlTd0e30=

Best,
Jason


--

Yue (Jason) Zhao

PhD Candidate, Bioinformatics Program

Boston University

yu...@bu.edu


On Mon, Mar 16, 2020 at 12:37 PM Shepherd, Lori 
mailto:lori.sheph...@roswellpark.org>>
 wrote:
I have just reinstalled Cairo on our builders and tested the install on both 
the 64-bit and 32-bit mode.  Hopefully this should clear up in tomorrows build 
report.  Please let us know if this continues to be an issue.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel 
mailto:bioc-devel-boun...@r-project.org>>
 on behalf of Yue Zhao (Jason) 
mailto:yu...@bu.edu>>
Sent: Monday, March 16, 2020 10:38 AM
To: bioc-devel 
mailto:bioc-devel@r-project.org>>
Subject: [Bioc-devel] Cairo error in Windows server

Hello Bioc Community,

The CHECK in the windows server throws an error message that is not seen in
other platforms and local windows computer:

Error: .onLoad failed in loadNamespace() for 'Cairo', details:
 call: library.dynam("Cairo", pkgname, libname)
 error: DLL 'Cairo' not found: maybe not installed for this architecture?


The link to the report:
https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_animalcules_tokay1-2Dchecksrc.html=DwICAg=iORugZls2LlYyCAZRB3XLg=basuzE7-VlMupNUhjOlOjq3Z71OZ7WVlqjvCai9jtug=RxM38Ya7V3JXYe8RL_frUAtwMB3VxNvWT0XwWo3r1QY=yO7r-OhxEb5J3NpMF_FR94z00WX5uqyv-3rRlTd0e30=

We have tired to find solutions, but it seems like a problem with the
windows server at Bioc? Please let me know if you have some advice, I
really appreciate it.

Thanks!

Best,
Jason


*--*

*Yue (Jason) Zhao*

PhD Candidate, Bioinformatics Program

Boston University

yu...@bu.edu

   [[alternative HTML version deleted]]

___
Bioc-devel@r-project.org
 mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=iORugZls2LlYyCAZRB3XLg=basuzE7-VlMupNUhjOlOjq3Z71OZ7WVlqjvCai9jtug=RxM38Ya7V3JXYe8RL_frUAtwMB3VxNvWT0XwWo3r1QY=VzgHbdfxzpav42pyeFxXF9gar3WLJjSjAWIb6gToITo=

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.


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, 

Re: [Bioc-devel] -fopenmp switch issue on mac

[Bunis, Daniel]

I was running into the `clang: *error: *unsupported option '-fopenmp’` 
yesterday myself.  I’m not on Sierra, but I fixed it with the top answer on 
this page: 
https://stackoverflow.com/questions/43595457/alternate-compiler-for-installing-r-packages-clang-error-unsupported-option/43943631#43943631?newreg=e3bd1c44b597485f981795398d9432b6.

Specifically, I used the solution #3 there to turn of the addition of the 
-fopenmp option:
1) Made a folder in my `~/` called .R
2) Made a file in ~/.R/Makevars containing:

SHLIB_OPENMP_CFLAGS=
SHLIB_OPENMP_CXXFLAGS=

Then I was able to install all the packages for which I’d been getting the 
-fopenmp error.

I hope this solution works for you as well!
-Dan

On Dec 4, 2019, at 8:07 AM, Kasper Daniel Hansen 
mailto:kasperdanielhan...@gmail.com>> wrote:

Are you using the clang 6 (R 3.5) / 7 (R 3.6) / 8 (R 4.0) which Simon
supplies?

This is for clang 6 with full path

/usr/local/clang6/bin/clang --version
clang version 6.0.0 (tags/RELEASE_600/final)
Target: x86_64-apple-darwin18.7.0
Thread model: posix
InstalledDir: /usr/local/clang6/bin

On Wed, Dec 4, 2019 at 11:03 AM Vincent Carey 
mailto:st...@channing.harvard.edu>>
wrote:

When installing packages from source,

I frequently run into this error with


%vjcair> clang --version

Apple LLVM version 9.0.0 (clang-900.0.39.2)

Target: x86_64-apple-darwin16.7.0

Thread model: posix

InstalledDir:

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin


I am still running macos Sierra ... is there a solution within this
platform?  I have been getting around this by modifying Makevars when
needed



* installing *source* package ‘sitmo’ ...

** package ‘sitmo’ successfully unpacked and MD5 sums checked

** using staged installation

** libs

clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
-I../inst/include/

-I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include'
-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
-I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c RcppExports.cpp -o
RcppExports.o

clang: *error: *unsupported option '-fopenmp'

make: *** [RcppExports.o] Error 1

ERROR: compilation failed for package ‘sitmo’

--
The information in this e-mail is intended only for th...{{dropped:15}}

___
Bioc-devel@r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=iORugZls2LlYyCAZRB3XLg=basuzE7-VlMupNUhjOlOjq3Z71OZ7WVlqjvCai9jtug=8ndw52WAHTohPcPQItPQQDlzi2GSSFsa48rBNYORZzQ=3Bk4CmiTOaGnnX2gf7KvkUvv3pW8P1ek4otRy5jvrPE=


[[alternative HTML version deleted]]

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