[Bioc-devel] Error in building vignette for previously stable version

[Jakob Willforss]

Hi all,


I am the developer of NormalyzerDE. A few days ago the release version of 
NormalyzerDE started getting errors in the vignette building (with no updates 
from my side). I saw in the mailing list that others also had encountered 
issues in the vignette. I don't know how widespread the issue is though.


Is this something I should try to address myself, or just leave it be for now?


I attach the error below.


Best wishes,

Jakob


* checking for file �NormalyzerDE/DESCRIPTION� ... OK
* preparing �NormalyzerDE�:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building �vignette.Rmd� using rmarkdown
Warning in file(con, "r") :
  file("") only supports open = "w+" and open = "w+b": using the former
! LaTeX Error: Command \VerbBar already defined.
   Or name \end... illegal, see p.192 of the manual.

Error: processing vignette 'vignette.Rmd' failed with diagnostics:
Failed to compile vignette.tex. See https://yihui.name/tinytex/r/#debugging for 
debugging tips. See vignette.log for more info.
--- failed re-building �vignette.Rmd�

SUMMARY: processing the following file failed:
  �vignette.Rmd�

Error: Vignette re-building failed.
Execution halted


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Re: [Bioc-devel] Bioconductor package twilight

[Stefanie Senger]

Hi Lori,


I just tried to clone to Github and understand I need BioC Git
credentials to do so, however I was not able to activate my account and
got the following message on
https://git.bioconductor.org/BiocCredentials/account_activation/


stefanie.sch...@gmx.de is not associated with a maintainer of a
Bioconductor package. Please check the spelling or contact
bioc-devel@r-project.org for help.


Which is weird since I got your e-mail below to that address. Could you
please help?


Thanks so much,
Stefanie




On 11/25/2019 8:32 AM, Shepherd, Lori wrote:
> Hello Bioconductor maintainer,
>
> R 4.0 has greater restrictions on registering/declaring S3 methods in
> the NAMESPACE. �The package you maintain is currently failing across
> all platforms in devel Bioconductor 3.11 because of unregistered
> methods. �The solution is quite simple and involves adding the method
> to the NAMESPACE file in the form of
>
> S3method(, ).
>
> You can see more information and other common build report failures
> and solutions posted on the Bioconductor Troubleshooting webpage:
> http://bioconductor.org/developers/how-to/troubleshoot-build-report/
>
>
> Please push the solution as soon as possible to avoid package
> deprecation.
>
> Cheers,
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
> 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.

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[Bioc-devel] Build error

[Kumar, Ashwath]

Hello bioc-devel team,

I recently came across an error when the automatic bot was trying to build my 
package. The error only happens on OSX systems.

===

R CMD BUILD

===

* checking for file CSSQ/DESCRIPTION ... OK
* preparing CSSQ:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
  ---
* installing *source* package CSSQ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package DelayedArray required by SummarizedExperiment could not be found
Execution halted
ERROR: lazy loading failed for package CSSQ
* removing 
/private/var/folders/gh/37kcv9bj20v2qnpgxq14hh1cgq/T/RtmpoFOgpq/Rinst54d57fc11079/CSSQ
  ---
ERROR: package installation failed


I am not sure how I can go about working on this specially since I do not have 
access to an OSX system. Can anyone advice on a way to go about dealing with 
this?

Note: The package did build properly multiple times before. This happened after 
I implemented some changes as suggested by reviewer. I am not sure if that is 
what is causing the issue.

Thanks,
Ashwath

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Re: [Bioc-devel] RangedData objects deprecated

[Vincent Carey]

The RangedData objects are still viable with the software you are using,
but trying
to set colnames will trigger an error.  In Bioc 3.11 you won't even be able
to use
the RangedData class at all.  So an intervention is needed now.

The RangedData objects that were serialized or created in your workflow
should
be converted to GRanges or GRangesList as appropriate, using as(...,
"GRanges")

Code that attempts to set the column names can be changed to use
colnames(mcols(...))

The ichorCNA package man pages don't include examples and I see no example
data with the package.

You might get a sense of what needs to be done in the following.

library(GenomicRanges)

ranges <- IRanges(c(1,2,3),c(4,5,6))

filter <- c(1L, 0L, 1L)

score <- c(10L, 2L, NA)


## constructing RangedData instances

## no variables

rd <- RangedData(ranges, filter, vals = score) # will not work at all

   # in Bioc 3.11

gr = as(rd, "GRanges")

colnames(mcols(gr))




On Wed, Dec 4, 2019 at 7:34 PM Brent O'Carrigan <
brent.ocarri...@cruk.cam.ac.uk> wrote:

> Dear Bioc devel team,
>
> Can you advise how to amend the following code to update references to
> RangedData objects?
>
> I’m running the Broad ichorCNA, which had a similar issue described in the
> package internal code, which I gather has been addressed
> https://github.com/broadinstitute/ichorCNA/issues/50
>
> A colleague has written a wrapper script in part of our shared pipeline,
> which I think was under R 3.5.3, and I think the RangedData references in
> this script may need updating  - which I have not been able to do.
>
> Kind regards,
>
> Dr Brent O'Carrigan
> Clinical Research Training Fellow | PhD candidate
> CRUK Cambridge Institute | Caldas Group
> Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE
> E: brent.ocarri...@cruk.cam.ac.uk
> | T: (+44) 01223 769500
>
> > source('make.ichor.summary.R')
> data.table 1.12.6 using 10 threads (see ?getDTthreads).  Latest news:
> r-datatable.com
> Loading required package: HMMcopy
> Loading required package: IRanges
> Loading required package: BiocGenerics
> Loading required package: parallel
>
> Attaching package: ‘BiocGenerics’
>
> The following objects are masked from ‘package:parallel’:
>
> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
> clusterExport, clusterMap, parApply, parCapply, parLapply,
> parLapplyLB, parRapply, parSapply, parSapplyLB
>
> The following objects are masked from ‘package:stats’:
>
> IQR, mad, sd, var, xtabs
>
> The following objects are masked from ‘package:base’:
>
> anyDuplicated, append, as.data.frame, basename, cbind, colnames,
> dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
> grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
> order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
> rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
> union, unique, unsplit, which, which.max, which.min
>
> Loading required package: S4Vectors
> Loading required package: stats4
>
> Attaching package: ‘S4Vectors’
>
> The following objects are masked from ‘package:data.table’:
>
> first, second
>
> The following object is masked from ‘package:base’:
>
> expand.grid
>
>
> Attaching package: ‘IRanges’
>
> The following object is masked from ‘package:data.table’:
>
> shift
>
> Loading required package: geneplotter
> Loading required package: Biobase
> Welcome to Bioconductor
>
> Vignettes contain introductory material; view with
> 'browseVignettes()'. To cite Bioconductor, see
> 'citation("Biobase")', and for packages 'citation("pkgname")'.
>
> Loading required package: lattice
> Loading required package: annotate
> Loading required package: AnnotationDbi
> Loading required package: XML
> Loading required package: ichorCNA
>
> Attaching package: ‘ichorCNA’
>
> The following object is masked from ‘package:HMMcopy’:
>
> HMMsegment
>
> Loading required package: GenomicRanges
> Loading required package: GenomeInfoDb
> [1] "./ichor/ichor.default/raw/041V10.sorted.dedupped.RDS"
> [1] "Running ichorCNA"
> Error: RangedData objects are deprecated and the colnames setter for
>   RangedData objects is now defunct. Please migrate your code to use
>   GRanges or GRangesList objects instead. See IMPORTANT NOTE in
>   ?RangedData
> In addition: Warning messages:
> 1:   RangedData objects are deprecated. Please migrate your code to use
>   GRanges or GRangesList objects instead. See IMPORTANT NOTE in
>   ?RangedData
> 2:   RangedData objects are deprecated. Please migrate your code to use
>   GRanges or GRangesList objects instead. See IMPORTANT NOTE in
>   ?RangedData
> 3:   RangedData objects are deprecated. Please migrate your code to use
>   GRanges or GRangesList objects instead. See IMPORTANT NOTE in
>   ?RangedData
> 4:   RangedData objects are deprecated. Please migrate your code to use
>   GRanges or GRangesList objects instead. See 

[Bioc-devel] RangedData objects deprecated

[Brent O'Carrigan]

Dear Bioc devel team,

Can you advise how to amend the following code to update references to 
RangedData objects?

I’m running the Broad ichorCNA, which had a similar issue described in the 
package internal code, which I gather has been addressed
https://github.com/broadinstitute/ichorCNA/issues/50

A colleague has written a wrapper script in part of our shared pipeline, which 
I think was under R 3.5.3, and I think the RangedData references in this script 
may need updating  - which I have not been able to do.

Kind regards,

Dr Brent O'Carrigan
Clinical Research Training Fellow | PhD candidate
CRUK Cambridge Institute | Caldas Group
Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE
E: brent.ocarri...@cruk.cam.ac.uk | T: 
(+44) 01223 769500

> source('make.ichor.summary.R')
data.table 1.12.6 using 10 threads (see ?getDTthreads).  Latest news: 
r-datatable.com
Loading required package: HMMcopy
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:data.table’:

first, second

The following object is masked from ‘package:base’:

expand.grid


Attaching package: ‘IRanges’

The following object is masked from ‘package:data.table’:

shift

Loading required package: geneplotter
Loading required package: Biobase
Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: XML
Loading required package: ichorCNA

Attaching package: ‘ichorCNA’

The following object is masked from ‘package:HMMcopy’:

HMMsegment

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
[1] "./ichor/ichor.default/raw/041V10.sorted.dedupped.RDS"
[1] "Running ichorCNA"
Error: RangedData objects are deprecated and the colnames setter for
  RangedData objects is now defunct. Please migrate your code to use
  GRanges or GRangesList objects instead. See IMPORTANT NOTE in
  ?RangedData
In addition: Warning messages:
1:   RangedData objects are deprecated. Please migrate your code to use
  GRanges or GRangesList objects instead. See IMPORTANT NOTE in
  ?RangedData
2:   RangedData objects are deprecated. Please migrate your code to use
  GRanges or GRangesList objects instead. See IMPORTANT NOTE in
  ?RangedData
3:   RangedData objects are deprecated. Please migrate your code to use
  GRanges or GRangesList objects instead. See IMPORTANT NOTE in
  ?RangedData
4:   RangedData objects are deprecated. Please migrate your code to use
  GRanges or GRangesList objects instead. See IMPORTANT NOTE in
  ?RangedData
5:   RangedData objects are deprecated. Please migrate your code to use
  GRanges or GRangesList objects instead. See IMPORTANT NOTE in
  ?RangedData
6:   RangedData objects are deprecated. Please migrate your code to use
  GRanges or GRangesList objects instead. See IMPORTANT NOTE in
  ?RangedData
7:   RangedData objects are deprecated. Please migrate your code to use
  GRanges or GRangesList objects instead. See IMPORTANT NOTE in
  ?RangedData
8:   RangedData objects are deprecated. Please migrate your code to use
  GRanges or GRangesList objects instead. See IMPORTANT NOTE in
  ?RangedData


> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /home/bioinformatics/software/R/R-3.6.1/lib64/R/lib/libRblas.so
LAPACK: /home/bioinformatics/software/R/R-3.6.1/lib64/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_GB.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=en_GB.UTF-8LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=en_GB.UTF-8LC_MESSAGES=en_GB.UTF-8
 [7] LC_PAPER=en_GB.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base 

Re: [Bioc-devel] Windows only vignette error - any ideas?

[Andrzej Oleś]

To me this issue doesn't seem to be directly linked to BiocStyle as the
affected package does not depend on it. Might be still a problem with
rmarkdown though.

Cheers,
Andrzej

On Wed, Dec 4, 2019 at 10:12 PM Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:

> We are hoping it is related to this:
> https://stat.ethz.ch/pipermail/bioc-devel/2019-December/015870.html so
> you should just sit tight.
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Bioc-devel  on behalf of
> Christopher John 
> Sent: Wednesday, December 4, 2019 2:05 AM
> To: bioc-devel@r-project.org 
> Subject: [Bioc-devel] Windows only vignette error - any ideas?
>
> Hi
>
> Since this morning I am getting an error for the Windows build only of my
> M3C package, shown below.
>
> Could anyone help please?
>
> Thanks,
>
> Chris
>
> * checking for file 'M3C/DESCRIPTION' ... OK
> * preparing 'M3C':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> --- re-building 'M3Cvignette.Rmd' using rmarkdown
> ! Package ifvtex Error: Name clash, \ifvtex is already defined.
>
> Error: processing vignette 'M3Cvignette.Rmd' failed with diagnostics:
> Failed to compile M3Cvignette.tex. See
> https://yihui.name/tinytex/r/#debugging for debugging tips. See
> M3Cvignette.log for more info.
> --- failed re-building 'M3Cvignette.Rmd'
>
> SUMMARY: processing the following file failed:
>   'M3Cvignette.Rmd'
>
> Error: Vignette re-building failed.
> Execution halted
>
> [[alternative HTML version deleted]]
>
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>
>
> 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.
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>
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Re: [Bioc-devel] Windows only vignette error - any ideas?

[Shepherd, Lori]

We are hoping it is related to this:  
https://stat.ethz.ch/pipermail/bioc-devel/2019-December/015870.html so you 
should just sit tight.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Christopher 
John 
Sent: Wednesday, December 4, 2019 2:05 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Windows only vignette error - any ideas?

Hi

Since this morning I am getting an error for the Windows build only of my
M3C package, shown below.

Could anyone help please?

Thanks,

Chris

* checking for file 'M3C/DESCRIPTION' ... OK
* preparing 'M3C':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'M3Cvignette.Rmd' using rmarkdown
! Package ifvtex Error: Name clash, \ifvtex is already defined.

Error: processing vignette 'M3Cvignette.Rmd' failed with diagnostics:
Failed to compile M3Cvignette.tex. See
https://yihui.name/tinytex/r/#debugging for debugging tips. See
M3Cvignette.log for more info.
--- failed re-building 'M3Cvignette.Rmd'

SUMMARY: processing the following file failed:
  'M3Cvignette.Rmd'

Error: Vignette re-building failed.
Execution halted

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Re: [Bioc-devel] Fwd: TVTB problems reported in the Multiple platform build/check report for BioC 3.10

[Martin Morgan]

I think it is this 
https://stat.ethz.ch/pipermail/bioc-devel/2019-December/015870.html so you 
should just sit tight...

On 12/5/19, 7:39 AM, "Bioc-devel on behalf of Kevin RUE" 
 wrote:

Hi,

I've been getting a weird Latex-related error on the daily build recently,
_although I haven't updated the package in ages_.

https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/TVTB/malbec1-buildsrc.html

I'm guessing some LaTeX package must have been updated recently and causes
trouble.
I'll have a look now, but any insights are welcome!

Kevin

I could switch the vignette over to PDF, but I prefer

-- Forwarded message -
From: 
Date: Wed, Dec 4, 2019 at 8:00 PM
Subject: TVTB problems reported in the Multiple platform build/check report
for BioC 3.10
To: 


[This is an automatically generated email. Please don't reply.]

Hi TVTB maintainer,

According to the Multiple platform build/check report for BioC 3.10,
the TVTB package has the following problem(s):

  o ERROR for 'R CMD build' on malbec1. See the details here:


https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/TVTB/malbec1-buildsrc.html

Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org

Notes:

  * This was the status of your package at the time this email was sent to
you.
Given that the online report is updated daily (in normal conditions) you
could see something different when you visit the URL(s) above,
especially if
you do so several days after you received this email.

  * It is possible that the problems reported in this report are false
positives,
either because another package (from CRAN or Bioconductor) breaks your
package (if yours depends on it) or because of a Build System problem.
If this is the case, then you can ignore this email.

  * Please check the report again 24h after you've committed your changes
to the
package and make sure that all the problems have gone.

  * If you have questions about this report or need help with the
maintenance of your package, please use the Bioc-devel mailing list:

  https://bioconductor.org/help/mailing-list/

(all package maintainers are requested to subscribe to this list)

For immediate notification of package build status, please
subscribe to your package's RSS feed. Information is at:

https://bioconductor.org/developers/rss-feeds/

Thanks for contributing to the Bioconductor project!

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[Bioc-devel] Fwd: TVTB problems reported in the Multiple platform build/check report for BioC 3.10

[Kevin RUE]

Hi,

I've been getting a weird Latex-related error on the daily build recently,
_although I haven't updated the package in ages_.
https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/TVTB/malbec1-buildsrc.html

I'm guessing some LaTeX package must have been updated recently and causes
trouble.
I'll have a look now, but any insights are welcome!

Kevin

I could switch the vignette over to PDF, but I prefer

-- Forwarded message -
From: 
Date: Wed, Dec 4, 2019 at 8:00 PM
Subject: TVTB problems reported in the Multiple platform build/check report
for BioC 3.10
To: 


[This is an automatically generated email. Please don't reply.]

Hi TVTB maintainer,

According to the Multiple platform build/check report for BioC 3.10,
the TVTB package has the following problem(s):

  o ERROR for 'R CMD build' on malbec1. See the details here:

https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/TVTB/malbec1-buildsrc.html

Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org

Notes:

  * This was the status of your package at the time this email was sent to
you.
Given that the online report is updated daily (in normal conditions) you
could see something different when you visit the URL(s) above,
especially if
you do so several days after you received this email.

  * It is possible that the problems reported in this report are false
positives,
either because another package (from CRAN or Bioconductor) breaks your
package (if yours depends on it) or because of a Build System problem.
If this is the case, then you can ignore this email.

  * Please check the report again 24h after you've committed your changes
to the
package and make sure that all the problems have gone.

  * If you have questions about this report or need help with the
maintenance of your package, please use the Bioc-devel mailing list:

  https://bioconductor.org/help/mailing-list/

(all package maintainers are requested to subscribe to this list)

For immediate notification of package build status, please
subscribe to your package's RSS feed. Information is at:

https://bioconductor.org/developers/rss-feeds/

Thanks for contributing to the Bioconductor project!

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

[Vincent Carey]

Thanks -- the solution I used was to install the Simon-Urbanek-modified
distribution clang 8.0 from the page noted in my reply.

On Wed, Dec 4, 2019 at 3:10 PM Bunis, Daniel  wrote:

> 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 <
> 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 
> 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=
>
>
>

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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}}

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Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10

[Shepherd, Lori]

We will start the process and be in touch off the bioc mailing list.

We would require you officially take over as maintainer as all bioconductor 
packages require an active maintainer.  PathNet was failing and we reached out 
(several times) and deemed the package orphaned as we never heard back from the 
currently listed maintainer.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Ludwig Geistlinger 
Sent: Wednesday, December 4, 2019 1:32 PM
To: Shepherd, Lori ; bioc-devel@r-project.org 

Subject: Re: Final List of Deprecated Packages for Bioc3.10


Yes, I could do that if needed.


From: Shepherd, Lori 
Sent: Wednesday, December 4, 2019 1:28 PM
To: Ludwig Geistlinger; bioc-devel@r-project.org
Subject: Re: Final List of Deprecated Packages for Bioc3.10

***ATTENTION: This email came from an external source. Do not open attachments 
or click on links from unknown senders or unexpected emails.***

Are you volunteering to permanently take over as maintainer of this package?



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Ludwig Geistlinger 
Sent: Wednesday, December 4, 2019 1:22 PM
To: Shepherd, Lori ; bioc-devel@r-project.org 

Subject: Re: Final List of Deprecated Packages for Bioc3.10

Hi Lori,

Is it possible to undeprecate the "PathNet" package?
I just checked, the problem is a failing unit test, causing the otherwise well 
working package to fail R CMD check.

I fixed this here on a local clone of 
https://git.bioconductor.org/packages/PathNet
 and could push these minor changes if granted access.

The PathNet package implements a solid network-based enrichment method and the 
corresponding paper has some 50 citations - it would thus be unfortunate to see 
it gone.

Thanks,
Ludwig



From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Monday, October 7, 2019 9:41 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10

The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly.

The final list for the 3.10 release is as follows:

Maintainer requested deprecation:

Software:

SNPchip
GenomeGraphs
HTSanalyzeR
Rchemcpp
charm
Pbase


Experiment Data Package:

charmData



Unresponsive/not-maintained packages:

Software:

dSimer
flipflop
exomePeak
CNPBayes
brainImageR
plateCore
rHVDM
SEPA
condcomp
PathNet
scone
birte
mlm4omics
RnaSeqSampleSize


Experiment Data Package:

facopy.annot
allenpvc


Renaming The package CAMTHC is marked for deprecation. This package has been 
renamed to debCAM



The following Annotation Packages have been user requested deprecated:

MafDb.gnomADex.r2.0.1.GRCh38
MafDb.gnomAD.r2.0.1.GRCh38
MafDb.gnomADex.r2.0.1.hs37d5
MafDb.gnomAD.r2.0.1.hs37d5
They are replaced with

MafDb.gnomADex.r2.1.GRCh38
MafDb.gnomAD.r2.1.GRCh38
MafDb.gnomADex.r2.1.hs37d5
MafDb.gnomAD.r2.1.hs37d5


The Bioconductor team will continue to send emails out to packages that have 
been broken across all platforms for an extended period of time as those are 
packages that are up for immediate deprecation if not corrected in a timely 
fashion. Packages that are ERRORing and not fixed before the October 30th 3.10 
release will immediately be marked as deprecated in devel 3.11.

Thank you


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

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Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10

[Ludwig Geistlinger]

Yes, I could do that if needed.


From: Shepherd, Lori 
Sent: Wednesday, December 4, 2019 1:28 PM
To: Ludwig Geistlinger; bioc-devel@r-project.org
Subject: Re: Final List of Deprecated Packages for Bioc3.10

***ATTENTION: This email came from an external source. Do not open attachments 
or click on links from unknown senders or unexpected emails.***

Are you volunteering to permanently take over as maintainer of this package?



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Ludwig Geistlinger 
Sent: Wednesday, December 4, 2019 1:22 PM
To: Shepherd, Lori ; bioc-devel@r-project.org 

Subject: Re: Final List of Deprecated Packages for Bioc3.10

Hi Lori,

Is it possible to undeprecate the "PathNet" package?
I just checked, the problem is a failing unit test, causing the otherwise well 
working package to fail R CMD check.

I fixed this here on a local clone of 
https://git.bioconductor.org/packages/PathNet
 and could push these minor changes if granted access.

The PathNet package implements a solid network-based enrichment method and the 
corresponding paper has some 50 citations - it would thus be unfortunate to see 
it gone.

Thanks,
Ludwig



From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Monday, October 7, 2019 9:41 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10

The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly.

The final list for the 3.10 release is as follows:

Maintainer requested deprecation:

Software:

SNPchip
GenomeGraphs
HTSanalyzeR
Rchemcpp
charm
Pbase


Experiment Data Package:

charmData



Unresponsive/not-maintained packages:

Software:

dSimer
flipflop
exomePeak
CNPBayes
brainImageR
plateCore
rHVDM
SEPA
condcomp
PathNet
scone
birte
mlm4omics
RnaSeqSampleSize


Experiment Data Package:

facopy.annot
allenpvc


Renaming The package CAMTHC is marked for deprecation. This package has been 
renamed to debCAM



The following Annotation Packages have been user requested deprecated:

MafDb.gnomADex.r2.0.1.GRCh38
MafDb.gnomAD.r2.0.1.GRCh38
MafDb.gnomADex.r2.0.1.hs37d5
MafDb.gnomAD.r2.0.1.hs37d5
They are replaced with

MafDb.gnomADex.r2.1.GRCh38
MafDb.gnomAD.r2.1.GRCh38
MafDb.gnomADex.r2.1.hs37d5
MafDb.gnomAD.r2.1.hs37d5


The Bioconductor team will continue to send emails out to packages that have 
been broken across all platforms for an extended period of time as those are 
packages that are up for immediate deprecation if not corrected in a timely 
fashion. Packages that are ERRORing and not fixed before the October 30th 3.10 
release will immediately be marked as deprecated in devel 3.11.

Thank you


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

___
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This email message may contain legally privileged and/or confidential 
information. If you are not the intended recipient(s), or the employee or agent 
responsible for the delivery of this message to the intended recipient(s), you 
are hereby notified that any disclosure, copying, distribution, or use of this 
email message is prohibited. If you have received this message in error, please 
notify the sender immediately by e-mail and delete this email message from your 
computer. Thank you.

[[alternative HTML version deleted]]

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Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10

[Shepherd, Lori]

Are you volunteering to permanently take over as maintainer of this package?



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Ludwig Geistlinger 
Sent: Wednesday, December 4, 2019 1:22 PM
To: Shepherd, Lori ; bioc-devel@r-project.org 

Subject: Re: Final List of Deprecated Packages for Bioc3.10

Hi Lori,

Is it possible to undeprecate the "PathNet" package?
I just checked, the problem is a failing unit test, causing the otherwise well 
working package to fail R CMD check.

I fixed this here on a local clone of 
https://git.bioconductor.org/packages/PathNet and could push these minor 
changes if granted access.

The PathNet package implements a solid network-based enrichment method and the 
corresponding paper has some 50 citations - it would thus be unfortunate to see 
it gone.

Thanks,
Ludwig



From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Monday, October 7, 2019 9:41 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10

The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly.

The final list for the 3.10 release is as follows:

Maintainer requested deprecation:

Software:

SNPchip
GenomeGraphs
HTSanalyzeR
Rchemcpp
charm
Pbase


Experiment Data Package:

charmData



Unresponsive/not-maintained packages:

Software:

dSimer
flipflop
exomePeak
CNPBayes
brainImageR
plateCore
rHVDM
SEPA
condcomp
PathNet
scone
birte
mlm4omics
RnaSeqSampleSize


Experiment Data Package:

facopy.annot
allenpvc


Renaming The package CAMTHC is marked for deprecation. This package has been 
renamed to debCAM



The following Annotation Packages have been user requested deprecated:

MafDb.gnomADex.r2.0.1.GRCh38
MafDb.gnomAD.r2.0.1.GRCh38
MafDb.gnomADex.r2.0.1.hs37d5
MafDb.gnomAD.r2.0.1.hs37d5
They are replaced with

MafDb.gnomADex.r2.1.GRCh38
MafDb.gnomAD.r2.1.GRCh38
MafDb.gnomADex.r2.1.hs37d5
MafDb.gnomAD.r2.1.hs37d5


The Bioconductor team will continue to send emails out to packages that have 
been broken across all platforms for an extended period of time as those are 
packages that are up for immediate deprecation if not corrected in a timely 
fashion. Packages that are ERRORing and not fixed before the October 30th 3.10 
release will immediately be marked as deprecated in devel 3.11.

Thank you


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]

___
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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 
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Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10

[Ludwig Geistlinger]

Hi Lori,

Is it possible to undeprecate the "PathNet" package?
I just checked, the problem is a failing unit test, causing the otherwise well 
working package to fail R CMD check.

I fixed this here on a local clone of 
https://git.bioconductor.org/packages/PathNet and could push these minor 
changes if granted access.

The PathNet package implements a solid network-based enrichment method and the 
corresponding paper has some 50 citations - it would thus be unfortunate to see 
it gone.

Thanks,
Ludwig



From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Monday, October 7, 2019 9:41 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10

The Bioconductor Team is continuing to identify packages that will be 
deprecated in the next release to allow for the Bioconductor community to 
respond accordingly.

The final list for the 3.10 release is as follows:

Maintainer requested deprecation:

Software:

SNPchip
GenomeGraphs
HTSanalyzeR
Rchemcpp
charm
Pbase


Experiment Data Package:

charmData



Unresponsive/not-maintained packages:

Software:

dSimer
flipflop
exomePeak
CNPBayes
brainImageR
plateCore
rHVDM
SEPA
condcomp
PathNet
scone
birte
mlm4omics
RnaSeqSampleSize


Experiment Data Package:

facopy.annot
allenpvc


Renaming The package CAMTHC is marked for deprecation. This package has been 
renamed to debCAM



The following Annotation Packages have been user requested deprecated:

MafDb.gnomADex.r2.0.1.GRCh38
MafDb.gnomAD.r2.0.1.GRCh38
MafDb.gnomADex.r2.0.1.hs37d5
MafDb.gnomAD.r2.0.1.hs37d5
They are replaced with

MafDb.gnomADex.r2.1.GRCh38
MafDb.gnomAD.r2.1.GRCh38
MafDb.gnomADex.r2.1.hs37d5
MafDb.gnomAD.r2.1.hs37d5


The Bioconductor team will continue to send emails out to packages that have 
been broken across all platforms for an extended period of time as those are 
packages that are up for immediate deprecation if not corrected in a timely 
fashion. Packages that are ERRORing and not fixed before the October 30th 3.10 
release will immediately be marked as deprecated in devel 3.11.

Thank you


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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

[Kasper Daniel Hansen]

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 
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}}

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[Bioc-devel] -fopenmp switch issue on mac

[Vincent Carey]

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’

-- 
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Re: [Bioc-devel] Activating git credentials

[Turaga, Nitesh]

It's possible your university is blocking emails. But either way, I've set a 
password for you and reset your account. 

You should receive a private email.

Once you add your SSH keys, you'll have access to your package.

Best,

Nitesh 


> On Dec 4, 2019, at 10:10 AM, Turaga, Nitesh  
> wrote:
> 
> You never activated the account earlier. This will be your first time, so you 
> don't have a password. 
> 
> I see, it could be that the "username" section of your email is 
> case-sensitive. I just sent you a test email, can you confirm if you've 
> received it? If you have we can assume that the email is NOT case-sensitive. 
> 
> Best,
> 
> Nitesh 
> 
> 
> 
>> On Dec 4, 2019, at 10:04 AM, Pages Gallego, M. 
>>  wrote:
>> 
>> Hi Nitesh,
>> 
>> thanks for your help. I have checked the junk folder, but nothing there. In 
>> principle no e-mail is sent since the error says that there is maintainer 
>> associated with the email. Perhaps a stupid question, but could it be that 
>> the error comes because I have uppercase characters? The error returns the 
>> email string all in lowercase.
>> 
>> I have also tried the forgot password option, in case I had already 
>> activated it and forgot about it. But it was not the case since I did not 
>> get any emails, also not in the junk folder.
>> 
>> Best,
>> Marc
>> 
>> On 04/12/2019, 15:54, "Turaga, Nitesh"  
>> wrote:
>> 
>>   Hi Marc,
>> 
>>   Your email address is associated with your package. 
>> "m.pagesgall...@umcutrecht.nl"
>> 
>>   You should be able to activate it from BiocCredentials. Have you tried 
>> checking in your spam folder or junk folder for the activation email?
>> 
>>   https://git.bioconductor.org/BiocCredentials
>> 
>>   It seems everything on my end looks fine. 
>> 
>>   Best,
>> 
>>   Nitesh 
>> 
>>> On Dec 4, 2019, at 3:53 AM, Pages Gallego, M. 
>>>  wrote:
>>> 
>>> Hi all,
>>> 
>>> I am trying to activate my Bioconductor Git Credentials account. When 
>>> trying it gives an error saying that the email address is not associated 
>>> with a package maintainer. However, I am the maintainer of 
>>> pulsedSilac
>>>  and I am using the same email address as stated in the description 
>>> file/Bioconductor webpage. I have also tried the email address associated 
>>> with my GitHub account but that gives the same error. Could I get some help 
>>> activating my credentials? Thanks in advance.
>>> 
>>> Best regards,
>>> Marc
>>> 
>>> 
>>> --
>>> 
>>> De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
>>> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
>>> ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct
>>> te informeren door het bericht te retourneren. Het Universitair Medisch
>>> Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de 
>>> W.H.W.
>>> (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd 
>>> bij
>>> de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
>>> 
>>> Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
>>> 
>>> --
>>> 
>>> This message may contain confidential information and is intended 
>>> exclusively
>>> for the addressee. If you receive this message unintentionally, please do 
>>> not
>>> use the contents but notify the sender immediately by return e-mail. 
>>> University
>>> Medical Center Utrecht is a legal person by public law and is registered at
>>> the Chamber of Commerce for Midden-Nederland under no. 30244197.
>>> 
>>> Please consider the environment before printing this e-mail.
>>> 
>>> [[alternative HTML version deleted]]
>>> 
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
>> 
>> 
>>   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, 
> 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 

Re: [Bioc-devel] Activating git credentials

[Turaga, Nitesh]

You never activated the account earlier. This will be your first time, so you 
don't have a password. 

I see, it could be that the "username" section of your email is case-sensitive. 
I just sent you a test email, can you confirm if you've received it? If you 
have we can assume that the email is NOT case-sensitive. 

Best,

Nitesh 



> On Dec 4, 2019, at 10:04 AM, Pages Gallego, M.  
> wrote:
> 
> Hi Nitesh,
> 
> thanks for your help. I have checked the junk folder, but nothing there. In 
> principle no e-mail is sent since the error says that there is maintainer 
> associated with the email. Perhaps a stupid question, but could it be that 
> the error comes because I have uppercase characters? The error returns the 
> email string all in lowercase.
> 
> I have also tried the forgot password option, in case I had already activated 
> it and forgot about it. But it was not the case since I did not get any 
> emails, also not in the junk folder.
> 
> Best,
> Marc
> 
> On 04/12/2019, 15:54, "Turaga, Nitesh"  wrote:
> 
>Hi Marc,
> 
>Your email address is associated with your package. 
> "m.pagesgall...@umcutrecht.nl"
> 
>You should be able to activate it from BiocCredentials. Have you tried 
> checking in your spam folder or junk folder for the activation email?
> 
>https://git.bioconductor.org/BiocCredentials
> 
>It seems everything on my end looks fine. 
> 
>Best,
> 
>Nitesh 
> 
>> On Dec 4, 2019, at 3:53 AM, Pages Gallego, M.  
>> wrote:
>> 
>> Hi all,
>> 
>> I am trying to activate my Bioconductor Git Credentials account. When trying 
>> it gives an error saying that the email address is not associated with a 
>> package maintainer. However, I am the maintainer of 
>> pulsedSilac
>>  and I am using the same email address as stated in the description 
>> file/Bioconductor webpage. I have also tried the email address associated 
>> with my GitHub account but that gives the same error. Could I get some help 
>> activating my credentials? Thanks in advance.
>> 
>> Best regards,
>> Marc
>> 
>> 
>> --
>> 
>> De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
>> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
>> ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct
>> te informeren door het bericht te retourneren. Het Universitair Medisch
>> Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de 
>> W.H.W.
>> (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd 
>> bij
>> de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
>> 
>> Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
>> 
>> --
>> 
>> This message may contain confidential information and is intended exclusively
>> for the addressee. If you receive this message unintentionally, please do not
>> use the contents but notify the sender immediately by return e-mail. 
>> University
>> Medical Center Utrecht is a legal person by public law and is registered at
>> the Chamber of Commerce for Midden-Nederland under no. 30244197.
>> 
>> Please consider the environment before printing this e-mail.
>> 
>>  [[alternative HTML version deleted]]
>> 
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
> 
>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, 
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.
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Re: [Bioc-devel] Activating git credentials

[Pages Gallego, M.]

Hi Nitesh,

thanks for your help. I have checked the junk folder, but nothing there. In 
principle no e-mail is sent since the error says that there is maintainer 
associated with the email. Perhaps a stupid question, but could it be that the 
error comes because I have uppercase characters? The error returns the email 
string all in lowercase.

I have also tried the forgot password option, in case I had already activated 
it and forgot about it. But it was not the case since I did not get any emails, 
also not in the junk folder.

Best,
Marc

On 04/12/2019, 15:54, "Turaga, Nitesh"  wrote:

Hi Marc,

Your email address is associated with your package. 
"m.pagesgall...@umcutrecht.nl"

You should be able to activate it from BiocCredentials. Have you tried 
checking in your spam folder or junk folder for the activation email?

https://git.bioconductor.org/BiocCredentials

It seems everything on my end looks fine. 

Best,

Nitesh 

> On Dec 4, 2019, at 3:53 AM, Pages Gallego, M. 
 wrote:
> 
> Hi all,
> 
> I am trying to activate my Bioconductor Git Credentials account. When 
trying it gives an error saying that the email address is not associated with a 
package maintainer. However, I am the maintainer of 
pulsedSilac
 and I am using the same email address as stated in the description 
file/Bioconductor webpage. I have also tried the email address associated with 
my GitHub account but that gives the same error. Could I get some help 
activating my credentials? Thanks in advance.
> 
> Best regards,
> Marc
> 
> 
> 
--
> 
> De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
> ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender 
direct
> te informeren door het bericht te retourneren. Het Universitair Medisch
> Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de 
W.H.W.
> (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat 
geregistreerd bij
> de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
> 
> Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
> 
> 
--
> 
> This message may contain confidential information and is intended 
exclusively
> for the addressee. If you receive this message unintentionally, please do 
not
> use the contents but notify the sender immediately by return e-mail. 
University
> Medical Center Utrecht is a legal person by public law and is registered 
at
> the Chamber of Commerce for Midden-Nederland under no. 30244197.
> 
> Please consider the environment before printing this e-mail.
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel



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.


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Re: [Bioc-devel] Activating git credentials

[Turaga, Nitesh]

Hi Marc,

Your email address is associated with your package. 
"m.pagesgall...@umcutrecht.nl"

You should be able to activate it from BiocCredentials. Have you tried checking 
in your spam folder or junk folder for the activation email?

https://git.bioconductor.org/BiocCredentials

It seems everything on my end looks fine. 

Best,

Nitesh 

> On Dec 4, 2019, at 3:53 AM, Pages Gallego, M.  
> wrote:
> 
> Hi all,
> 
> I am trying to activate my Bioconductor Git Credentials account. When trying 
> it gives an error saying that the email address is not associated with a 
> package maintainer. However, I am the maintainer of 
> pulsedSilac
>  and I am using the same email address as stated in the description 
> file/Bioconductor webpage. I have also tried the email address associated 
> with my GitHub account but that gives the same error. Could I get some help 
> activating my credentials? Thanks in advance.
> 
> Best regards,
> Marc
> 
> 
> --
> 
> De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
> ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct
> te informeren door het bericht te retourneren. Het Universitair Medisch
> Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de 
> W.H.W.
> (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij
> de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.
> 
> Denk s.v.p aan het milieu voor u deze e-mail afdrukt.
> 
> --
> 
> This message may contain confidential information and ...{{dropped:28}}

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Re: [Bioc-devel] Error in Vignette of package

[Andrzej Oleś]

Dear Package Developers,

BiocStyle will be patched within the next couple of days to address the
observed errors. Until then please refrain from making any changes to your
package, the issue should resolve itself once BiocStyle is updated.

Cheers,
Andrzej

On Mon, Dec 2, 2019 at 11:20 AM Andrzej Oleś  wrote:

> Hi,
>
> the error seems to be related to some recent changes in the upstream
> package rmarkdown v1.18. I will give you an update once I know more details.
>
> Cheers,
> Andrzej
>
>
> On Sun, Dec 1, 2019 at 5:00 PM Benjamin Jean-Marie Tremblay <
> b2tremb...@uwaterloo.ca> wrote:
>
>> Not using BiocStyle::pdf_document means you can’t use the helpers/macros.
>> Try this in a fresh interactive session:
>>
>>   library(BiocStyle)
>>   rmarkdown::render("yourvignette.Rmd")
>>
>> This should make the helpers/macros available. It won’t fix the issue
>> for passing R CMD check, but at least it’ll confirm what the issue is and
>> thus you’ll know to wait for BiocStyle to update.
>>
>> BT
>>
>> > Le 1 déc. 2019 à 10:47, Ioannis Vardaxis  a écrit :
>> >
>> > Thanks for the answer. However replacing it resulted in another error
>> for me:
>> >
>> > Quitting from lines 2-41 (MACPET.Rmd)
>> > Error in doc_date() : could not find function "doc_date"
>> > Calls:  ... inline_exec -> hook_eval -> withVisible -> eval
>> -> eval
>> > Execution halted
>> >
>> > Should I wait until BiocStyle is updated?
>> >
>> > Best,
>> > Ioannis
>> >
>> > Fra: Martin Morgan 
>> > Sendt: søndag 1. desember 2019 11:51
>> > Til: Benjamin Jean-Marie Tremblay ; Ioannis
>> Vardaxis 
>> > Kopi: bioc-devel@r-project.org 
>> > Emne: Re: [Bioc-devel] Error in Vignette of package
>> >
>> > Thanks for that insight, we'll try to solve the issue with BiocStyle.
>> >
>> > Martin
>> >
>> > On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie
>> Tremblay" > b2tremb...@uwaterloo.ca> wrote:
>> >
>> > I’ve been getting the exact same error for compiling the Rmarkdown
>> > vignettes in my own package. Some partial testing before the weekend
>> > revealed that in my case the error could be circumvented simply by
>> not
>> > using
>> >
>> > output: BiocStyle::pdf_document
>> >
>> > but instead
>> >
>> > output: pdf_document
>> >
>> > in the yaml header. I’m not quite sure why, but when BiocStyle is
>> used
>> > some of the latex code for code highlighting is repeated, leading
>> to the
>> > 'already defined' error. I’ve not updated my package since before
>> this
>> > error started.
>> >
>> > BT
>> >
>> > > Le 30 nov. 2019 à 10:25, Ioannis Vardaxis  a
>> écrit :
>> > >
>> > > Hey,
>> > >
>> > > I am trying to build my package Vegnette and I get the following
>> error:
>> > >
>> > > ! LaTeX Error: Command \VerbBar already defined.
>> > >   Or name \end... illegal, see p.192 of the manual.
>> > >
>> > > I tried to find what this means with no luck.
>> > >
>> > > Best,
>> > > Ioannis
>> > >
>> > >
>> > >[[alternative HTML version deleted]]
>> > >
>> > > ___
>> > > Bioc-devel@r-project.org mailing list
>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>

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[Bioc-devel] jupyter installation on merida1

[Angerer, Philipp]

Dear BioConductor maintainers, 

The buildbots almost seem able to build my package’s vignettes again, but the 
jupyter installation on merida1 still [ 
http://bioconductor.org/checkResults/release/bioc-LATEST/destiny/merida1-buildsrc.html
 | doesn’t seem quite right ] : 
* creating vignettes ... ERROR 
--- re-building ‘DPT.ipynbmeta’ using nbconvert 
Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = 
env,  : 
running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' [...] 'DPT.ipynb' 2>&1' 
had status 126 
Call failed. Output: 
sh: /usr/local/bin/jupyter: /usr/local/opt/python3/bin/python3.6: bad 
interpreter: No such file or directory 


Exit status 126 means “The thing you tried to execute is not executable or 
doesn’t exist”. The message looks like sh tries to find the binary referenced 
in the shebang of /usr/local/bin/jupyter, and fails. I assume jupyter has been 
installed with an interpreter that no longer exists, and now its shebang points 
into the void? I guess the following is true for your system: 
$ head -n1 /usr/local/bin/jupyter 
#!/usr/local/opt/python3/bin/python3.6 
$ ls /usr/local/opt/python3/bin/python3.6 
No such file or directory (os error 2) 


Anyway, it would be amazing if someone could fix jupyter’s installation on that 
system (until jupyter nbconvert --help works). The vignette engine trying to 
use it (nbconvertR) [ https://cran.rstudio.com/web/packages/nbconvertR/INSTALL 
| has extensive INSTALL instructions ] that might help! 


Thank you so much, 
Philipp 

Helmholtz Zentrum München


Helmholtz Zentrum München


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[Bioc-devel] Activating git credentials

[Pages Gallego, M.]

Hi all,

I am trying to activate my Bioconductor Git Credentials account. When trying it 
gives an error saying that the email address is not associated with a package 
maintainer. However, I am the maintainer of 
pulsedSilac
 and I am using the same email address as stated in the description 
file/Bioconductor webpage. I have also tried the email address associated with 
my GitHub account but that gives the same error. Could I get some help 
activating my credentials? Thanks in advance.

Best regards,
Marc


--

De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is
uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht
ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct
te informeren door het bericht te retourneren. Het Universitair Medisch
Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W.
(Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij
de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197.

Denk s.v.p aan het milieu voor u deze e-mail afdrukt.

--

This message may contain confidential information and is intended exclusively
for the addressee. If you receive this message unintentionally, please do not
use the contents but notify the sender immediately by return e-mail. University
Medical Center Utrecht is a legal person by public law and is registered at
the Chamber of Commerce for Midden-Nederland under no. 30244197.

Please consider the environment before printing this e-mail.

[[alternative HTML version deleted]]

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