Re: [Bioc-devel] GEOmetadb package is missing "Organism" metadata field in all GSE accession IDs

[Vincent Carey]

You can get the information through the merged tables:

> dbListTables(con)

 [1] "gds"   "gds_subset""geoConvert"

 [4] "geodb_column_desc" "gpl"   "gse"

 [7] "gse_gpl"   "gse_gsm"   "gsm"

[10] "metaInfo"  "sMatrix"

> cdesc = dbReadTable(con, "geodb_column_desc")

> poten = grep("gani", cdesc[,2])

> cdesc[poten,]

   TableName FieldName

26   gpl  organism

49   gsm  organism_ch1

57   gsm  organism_ch2

77   gds platform_organism

80   gds   sample_organism

  Description

26 [Values separated by ';tab', if more than one] Organism(s)

49 organism(s) from which the biological material was derived

57   same contents as ch1

77   organism of the platform

80organism of the samples

On Sun, Oct 15, 2017 at 2:29 AM, Bohdan Khomtchouk 
wrote:

> library(GEOmetadb)
>
> if(!file.exists('GEOmetadb.sqlite')) getSQLiteFile()
>
> con <- dbConnect(SQLite(),'GEOmetadb.sqlite')
>
>
> dbListFields(con,'gse')
>
> ##  [1] "ID"   "title"
> ##  [3] "gse"  "status"
> ##  [5] "submission_date"  "last_update_date"
> ##  [7] "pubmed_id""summary"
> ##  [9] "type" "contributor"
> ## [11] "web_link" "overall_design"
> ## [13] "repeats"  "repeats_sample_list"
> ## [15] "variable" "variable_description"
> ## [17] "contact"  "supplementary_file"
>
>
> Clearly, there should also be an "Organism" metadata field, e.g.:
> https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4032
>
> Please advise.
>
> --
>
> Bohdan Khomtchouk, Ph.D.
>
> Postdoctoral Research Scholar, Gozani Lab
>
> Department of Biology, Stanford University
>
> Gilbert Building, Room 206
>
> 371 Serra Mall
>
> Stanford, CA 94305-5020
>
> https://profiles.stanford.edu/bohdan-khomtchouk
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

[[alternative HTML version deleted]]

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

Re: [Bioc-devel] EXTERNAL: Re: Bioconductor 3.6 release: update NEWS

[Obenchain, Valerie]

Hi,

You have a couple of options described on the ?news man page. The most common 
is to have a NEWS plain text file at the same level as DESCRIPTION, NAMESPACE, 
R etc. For examples, you could look at a variety of Bioconductor packages, 
GenomicRanges, IRanges, Rsamtools etc.

?news also describes the inst/NEWS.Rd approach where the .Rd file needs to 
follow standard formatting with \itemize, \subsection etc.

Thanks for pointing out the link on the Package Submission page. I think that 
should be updated to point to ?news.

Valerie




On 10/14/2017 08:05 AM, Stian L�gstad wrote:
Hi,

What should the NEWS file look like? Are there guidelines somewhere?

Also, where should it be located? This 
page says 
`inst/NEWS`, but I see many packages has the file at root level.

On Fri, Oct 13, 2017 at 5:16 PM, Obenchain, Valerie 
mailto:valerie.obench...@roswellpark.org>> 
wrote:
Package maintainers,

If you haven't already, please update the NEWS files in your packages. This 
information will be included in the release announcement. The deadline for 
updating NEWS files is Tuesday, October 24:

http://www.bioconductor.org/developers/release-schedule/

Thanks.

Valerie


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]]

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



--
Stian L�gstad
+47 41 80 80 25



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]]

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

Re: [Bioc-devel] EXTERNAL: Re: Bioconductor 3.6 release: update NEWS

[Obenchain, Valerie]

Sorry, didn't see Martin's response before sending.

Valerie


On 10/15/2017 07:17 AM, Obenchain, Valerie wrote:
Hi,

You have a couple of options described on the ?news man page. The most common 
is to have a NEWS plain text file at the same level as DESCRIPTION, NAMESPACE, 
R etc. For examples, you could look at a variety of Bioconductor packages, 
GenomicRanges, IRanges, Rsamtools etc.

?news also describes the inst/NEWS.Rd approach where the .Rd file needs to 
follow standard formatting with \itemize, \subsection etc.

Thanks for pointing out the link on the Package Submission page. I think that 
should be updated to point to ?news.

Valerie




On 10/14/2017 08:05 AM, Stian L�gstad wrote:
Hi,

What should the NEWS file look like? Are there guidelines somewhere?

Also, where should it be located? This 
page says 
`inst/NEWS`, but I see many packages has the file at root level.

On Fri, Oct 13, 2017 at 5:16 PM, Obenchain, Valerie 
mailto:valerie.obench...@roswellpark.org>> 
wrote:
Package maintainers,

If you haven't already, please update the NEWS files in your packages. This 
information will be included in the release announcement. The deadline for 
updating NEWS files is Tuesday, October 24:

http://www.bioconductor.org/developers/release-schedule/

Thanks.

Valerie


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]]

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



--
Stian L�gstad
+47 41 80 80 25




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]]

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

Re: [Bioc-devel] EXTERNAL: Re: Cannot move 'xps' to GIT

[cstrato]

Hi,

Since 'https://github.com/cstrato/xps' does only contain information how 
to create or push a repository I tried to follow again:



http://master.bioconductor.org/developers/how-to/git/push-to-github-bioc/


2. View existing remotes
$ git remote -v
origin  g...@github.com:cstrato/xps.git (fetch)
origin  g...@github.com:cstrato/xps.git (push)
upstreamg...@git.bioconductor.org:packages/xps.git (fetch)
upstreamg...@git.bioconductor.org:packages/xps.git (push)


3. Make and commit changes to the master branch
$ git checkout master
M   DESCRIPTION
M   NEWS
M   configure.in
Already on 'master'
Your branch is up-to-date with 'origin/master'.
# edit files, etc.
$ git add -v DESCRIPTION
$ git add -v NEWS
$ git add -v configure.in



When running 'commit' I got the following information, which is not 
clear to me:


$ git commit -m "update for configure.in"
[master 7a9855f] update for configure.in
 Committer: rabbitus 
Your name and email address were configured automatically based
on your username and hostname. Please check that they are accurate.
You can suppress this message by setting them explicitly. Run the
following command and follow the instructions in your editor to edit
your configuration file:

git config --global --edit

After doing this, you may fix the identity used for this commit with:

git commit --amend --reset-author

 3 files changed, 62 insertions(+), 58 deletions(-)



So I tried:

$ git config --global --edit
# This is Git's per-user configuration file.
[user]
# Please adapt and uncomment the following lines:
#   name = rabbitus
#   email = rabbitus@lumimacs-iMac.local


and changed the '.gitconfig' file to:
# This is Git's per-user configuration file.
[user]
# Please adapt and uncomment the following lines:
#   name = cstrato
#   email = cstr...@aon.at



It is not clear to me whether I have to change my name/email or keep the 
original one.


Could you tell me which one should be the correct one?



Then I did run:

$ git commit --amend --reset-author
# Please enter the commit message for your changes. Lines starting
# with '#' will be ignored, and an empty message aborts the commit.
#
# Committer: rabbitus 
#
# On branch master
# Your branch is ahead of 'origin/master' by 1 commit.
#   (use "git push" to publish your local commits)
#
# Changes to be committed:
#   modified:   DESCRIPTION
#   modified:   NEWS
#   modified:   configure.in


In this case I did not change anything, since I am not sure what it means.

Can you explain what this means, since 
'https://git-scm.com/docs/git-commit' did not help me.


Should I change this file?



Then I did steps 5 and 6 and got the following:

5. Push updates to GitHub's (origin) master branch
$ git push origin master
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.


6. Next, push updates to Bioconductor's (upstream) master branch
$ git push upstream master
Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
Counting objects: 5, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (5/5), done.
Writing objects: 100% (5/5), 727 bytes | 0 bytes/s, done.
Total 5 (delta 4), reused 0 (delta 0)
To git.bioconductor.org:packages/xps.git
   d63ffaf..d83779f  master -> master



Finally I did:

$ ssh -v g...@git.bioconductor.org/packages/xps
OpenSSH_7.4p1, LibreSSL 2.5.0
debug1: Reading configuration data /Users/rabbitus/.ssh/config
debug1: Reading configuration data /etc/ssh/ssh_config
ssh: Could not resolve hostname git: nodename nor servname provided, or 
not known



However, now I get only an ssh error message:


Do you know what I did wrong this time?


Thank you.
Best regards,
Christian


On 10/13/17 20:12, Turaga, Nitesh wrote:

Hi,

Both your `origin` and `upstream` are set to the same location i.e 
g...@git.bioconductor.org:packages/xps.

This is wrong. You want your origin to point to `g...@github.com:cstrato/xps`

You can do this by following the commands,

`git remote set-url origin g...@github.com:cstrato/xps.git`

`git push origin master`

All of this documentation is given in bioconductor.org/developers/how-to/git/.

Best,

Nitesh



On Oct 13, 2017, at 2:07 PM, cstrato  wrote:

Dear Martin,

Following your advice

   https://bioconductor.org/developers/how-to/git/maintain-github-bioc/

I did the following:

$ cd xps
$ git remote add upstream g...@git.bioconductor.org:packages/xps.git
$ git fetch upstream
Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
 From git.bioconductor.org:packages/xps
* [new branch]  RELEASE_2_10 -> upstream/RELEASE_2_10
* [new branch]  RELEASE_2_11 -> upstream/RELEASE_2_11
* [new branch]  RELEASE_2_12 -> upstream/RELEASE_2_12
* [new branch]  RELEASE_2_13 -> upstream/RELEASE_2_13
* [new branch]  RELEASE_2_14 -> upstream/RELEASE_2_14
* [new branch]  RELEASE_2_2 -> upstream

Re: [Bioc-devel] EXTERNAL: Re: Cannot move 'xps' to GIT

[cstrato]

I have just seen the update 2017-10-15 of the BUILD/CHECK report:

 http://bioconductor.org/checkResults/devel/bioc-LATEST/xps/

which was not available when I have sent my former mail.

For some reason my commit to version xps_1.37.2 was not accepted.

Please tell me what I need to do to solve this problem.

Best regards,
Christian



On 10/15/17 21:37, cstrato wrote:

Hi,

Since 'https://github.com/cstrato/xps' does only contain information how 
to create or push a repository I tried to follow again:



http://master.bioconductor.org/developers/how-to/git/push-to-github-bioc/


2. View existing remotes
$ git remote -v
origin  g...@github.com:cstrato/xps.git (fetch)
origin  g...@github.com:cstrato/xps.git (push)
upstream    g...@git.bioconductor.org:packages/xps.git (fetch)
upstream    g...@git.bioconductor.org:packages/xps.git (push)


3. Make and commit changes to the master branch
$ git checkout master
M   DESCRIPTION
M   NEWS
M   configure.in
Already on 'master'
Your branch is up-to-date with 'origin/master'.
# edit files, etc.
$ git add -v DESCRIPTION
$ git add -v NEWS
$ git add -v configure.in



When running 'commit' I got the following information, which is not 
clear to me:


$ git commit -m "update for configure.in"
[master 7a9855f] update for configure.in
  Committer: rabbitus 
Your name and email address were configured automatically based
on your username and hostname. Please check that they are accurate.
You can suppress this message by setting them explicitly. Run the
following command and follow the instructions in your editor to edit
your configuration file:

     git config --global --edit

After doing this, you may fix the identity used for this commit with:

     git commit --amend --reset-author

  3 files changed, 62 insertions(+), 58 deletions(-)



So I tried:

$ git config --global --edit
# This is Git's per-user configuration file.
[user]
# Please adapt and uncomment the following lines:
#   name = rabbitus
#   email = rabbitus@lumimacs-iMac.local


and changed the '.gitconfig' file to:
# This is Git's per-user configuration file.
[user]
# Please adapt and uncomment the following lines:
#   name = cstrato
#   email = cstr...@aon.at



It is not clear to me whether I have to change my name/email or keep the 
original one.


Could you tell me which one should be the correct one?



Then I did run:

$ git commit --amend --reset-author
# Please enter the commit message for your changes. Lines starting
# with '#' will be ignored, and an empty message aborts the commit.
#
# Committer: rabbitus 
#
# On branch master
# Your branch is ahead of 'origin/master' by 1 commit.
#   (use "git push" to publish your local commits)
#
# Changes to be committed:
#   modified:   DESCRIPTION
#   modified:   NEWS
#   modified:   configure.in


In this case I did not change anything, since I am not sure what it means.

Can you explain what this means, since 
'https://git-scm.com/docs/git-commit' did not help me.


Should I change this file?



Then I did steps 5 and 6 and got the following:

5. Push updates to GitHub's (origin) master branch
$ git push origin master
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.


6. Next, push updates to Bioconductor's (upstream) master branch
$ git push upstream master
Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
Counting objects: 5, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (5/5), done.
Writing objects: 100% (5/5), 727 bytes | 0 bytes/s, done.
Total 5 (delta 4), reused 0 (delta 0)
To git.bioconductor.org:packages/xps.git
    d63ffaf..d83779f  master -> master



Finally I did:

$ ssh -v g...@git.bioconductor.org/packages/xps
OpenSSH_7.4p1, LibreSSL 2.5.0
debug1: Reading configuration data /Users/rabbitus/.ssh/config
debug1: Reading configuration data /etc/ssh/ssh_config
ssh: Could not resolve hostname git: nodename nor servname provided, or 
not known



However, now I get only an ssh error message:


Do you know what I did wrong this time?


Thank you.
Best regards,
Christian


On 10/13/17 20:12, Turaga, Nitesh wrote:

Hi,

Both your `origin` and `upstream` are set to the same location i.e 
g...@git.bioconductor.org:packages/xps.


This is wrong. You want your origin to point to 
`g...@github.com:cstrato/xps`


You can do this by following the commands,

`git remote set-url origin g...@github.com:cstrato/xps.git`

`git push origin master`

All of this documentation is given in 
bioconductor.org/developers/how-to/git/.


Best,

Nitesh



On Oct 13, 2017, at 2:07 PM, cstrato  wrote:

Dear Martin,

Following your advice

   https://bioconductor.org/developers/how-to/git/maintain-github-bioc/

I did the following:

$ cd xps
$ git remote add upstream g...@git.bioconductor.org:packages/xps.git
$ git fetch upstream
Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa'

Re: [Bioc-devel] EXTERNAL: Re: Cannot move 'xps' to GIT

[Martin Morgan]

On 10/15/2017 06:00 PM, cstrato wrote:

I have just seen the update 2017-10-15 of the BUILD/CHECK report:

  http://bioconductor.org/checkResults/devel/bioc-LATEST/xps/

which was not available when I have sent my former mail.

For some reason my commit to version xps_1.37.2 was not accepted.

Please tell me what I need to do to solve this problem.


I guess you mean this commit

xps master$ git log -n 1
commit d83779f467f7ac6736f95f4f8b78839654ab1af2
Author: rabbitus 
Date:   Sun Oct 15 13:52:26 2017 +0200

update for configure.in

which is where the version bump occurred

xps master$ git show d83779f467f7ac6736f95f4f8b78839654ab1af2 DESCRIPTION
commit d83779f467f7ac6736f95f4f8b78839654ab1af2
Author: rabbitus 
Date:   Sun Oct 15 13:52:26 2017 +0200

update for configure.in

diff --git a/DESCRIPTION b/DESCRIPTION
index fb59243..af15fa0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: xps
-Version: 1.37.1
+Version: 1.37.2
 Title: Processing and Analysis of Affymetrix Oligonucleotide Arrays
 including Exon Arrays, Whole Genome Arrays and Plate Arrays
 Author: Christian Stratowa, Vienna, Austria


As you know, bioconductor builds are NIGHTLY. The build report you cite 
has a snapshot date of 2017-10-14 17:00:13 -0400 (Sat, 14 Oct 2017) so 
your commit cam after the snapshot.


Wait for the next build report.

Martin



Best regards,
Christian



On 10/15/17 21:37, cstrato wrote:

Hi,

Since 'https://github.com/cstrato/xps' does only contain information 
how to create or push a repository I tried to follow again:



http://master.bioconductor.org/developers/how-to/git/push-to-github-bioc/


2. View existing remotes
$ git remote -v
origin  g...@github.com:cstrato/xps.git (fetch)
origin  g...@github.com:cstrato/xps.git (push)
upstream    g...@git.bioconductor.org:packages/xps.git (fetch)
upstream    g...@git.bioconductor.org:packages/xps.git (push)


3. Make and commit changes to the master branch
$ git checkout master
M   DESCRIPTION
M   NEWS
M   configure.in
Already on 'master'
Your branch is up-to-date with 'origin/master'.
# edit files, etc.
$ git add -v DESCRIPTION
$ git add -v NEWS
$ git add -v configure.in



When running 'commit' I got the following information, which is not 
clear to me:


$ git commit -m "update for configure.in"
[master 7a9855f] update for configure.in
  Committer: rabbitus 
Your name and email address were configured automatically based
on your username and hostname. Please check that they are accurate.
You can suppress this message by setting them explicitly. Run the
following command and follow the instructions in your editor to edit
your configuration file:

 git config --global --edit

After doing this, you may fix the identity used for this commit with:

 git commit --amend --reset-author

  3 files changed, 62 insertions(+), 58 deletions(-)



So I tried:

$ git config --global --edit
# This is Git's per-user configuration file.
[user]
# Please adapt and uncomment the following lines:
#   name = rabbitus
#   email = rabbitus@lumimacs-iMac.local


and changed the '.gitconfig' file to:
# This is Git's per-user configuration file.
[user]
# Please adapt and uncomment the following lines:
#   name = cstrato
#   email = cstr...@aon.at



It is not clear to me whether I have to change my name/email or keep 
the original one.


Could you tell me which one should be the correct one?



Then I did run:

$ git commit --amend --reset-author
# Please enter the commit message for your changes. Lines starting
# with '#' will be ignored, and an empty message aborts the commit.
#
# Committer: rabbitus 
#
# On branch master
# Your branch is ahead of 'origin/master' by 1 commit.
#   (use "git push" to publish your local commits)
#
# Changes to be committed:
#   modified:   DESCRIPTION
#   modified:   NEWS
#   modified:   configure.in


In this case I did not change anything, since I am not sure what it 
means.


Can you explain what this means, since 
'https://git-scm.com/docs/git-commit' did not help me.


Should I change this file?



Then I did steps 5 and 6 and got the following:

5. Push updates to GitHub's (origin) master branch
$ git push origin master
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.


6. Next, push updates to Bioconductor's (upstream) master branch
$ git push upstream master
Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
Counting objects: 5, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (5/5), done.
Writing objects: 100% (5/5), 727 bytes | 0 bytes/s, done.
Total 5 (delta 4), reused 0 (delta 0)
To git.bioconductor.org:packages/xps.git
    d63ffaf..d83779f  master -> master



Finally I did:

$ ssh -v g...@git.bioconductor.org/packages/xps
OpenSSH_7.4p1, LibreSSL 2.5.0
debug1: Reading configuration data /Users/rabbitus/.ssh/config
debug1: Re

Re: [Bioc-devel] EXTERNAL: Increase timeout for mzR on Windows?

[Neumann, Steffen]

Hi,

On Sat, 2017-10-14 at 14:04 -0400, Kasper Daniel Hansen wrote:
> I recognize that the code base is pretty complex (and that mass spec
> libraries are a mess at times), but could there be advantages to
> modularizing the code into more than 1 package, with a mzR master
> package. Could that help with linking etc?

Currently I can't think of a way here. Basically, mzR uses 
one top-level object from "msdata" proteowizard, and we only include
and compile the minimum of dependencies for msdata. 

And indeed, today mzR finished in 1475 seconds on Windows, 
which is 1000 secs before the timeout would kick in. 

Not sure if upon the first compile after the fresh R installation
there is a cache built up by mingw somewhere, which would explain
why it is faster afterwards.

Yours,
Steffen



> 
> Best,
> Kasper
> 
> On Fri, Oct 13, 2017 at 4:24 PM, Neumann, Steffen  .de> wrote:
> > Hi,
> > 
> > we've had binary compiles a while ago, but we were glad
> > when we could revert that to "normal" compilation a long time ago.
> > 
> > Another observation from years ago was that the linker step
> > was what took the longest, and even with a precompiled libpwiz.a
> > this took very long.
> > 
> > Thanks Herve for the observation about normal build times
> > vs. the "fresh R" case. This might show that, in general,
> > mzR does build in <40 minutes.
> > 
> > yours,
> > Steffen
> > 
> > On Wed, 2017-10-11 at 09:39 -0400, Martin Morgan wrote:
> > > On 10/11/2017 08:29 AM, Laurent Gatto wrote:
> > > >
> > > > On 11 October 2017 11:14, Rainer Johannes wrote:
> > > >
> > > > > Dear Martin,
> > > > >
> > > > > > On 11 Oct 2017, at 13:05, Martin Morgan  > ellp
> > > > > > ark.org> wrote:
> > > > > >
> > > > > > On 10/11/2017 03:48 AM, Rainer Johannes wrote:
> > > > > > > Hi,
> > > > > > > would it be possible to increase the allowed build and
> > check
> > > > > > > times for mzR on Windows? Building mzR takes very long
> > due to
> > > > > > > the compilation of the included proteowizard (and boost?)
> > > > > > > code so there is not much we can do to speed that up.
> > > > > >
> > > > > > what's the role of proteowizard in mzR? is it required in
> > its
> > > > > > entirety, or can it be more selectively included? I agree
> > that
> > > > > > mzR is often problematic because of the excessive
> > compilation
> > > > > > time.
> > > > > >
> > > > >
> > > > > mzR uses Rcpp modules to directly call/use the C++ code from
> > > > > proteowizard to read mzML, mzXML and other MS file formats.
> > > > > Regarding
> > > > > selective includes: I believe Steffen Neumann and Laurent
> > Gatto
> > > > > spent
> > > > > already a great deal of time to reduce the amount of code
> > that
> > > > > needs
> > > > > to be included for mzR to compile/work. I think there is not
> > much
> > > > > more
> > > > > that can be done here, unfortunately.
> > > >
> > > > Steffen (he should get the credit for this) has indeed tried to
> > be
> > > > as
> > > > selective as possible, yes. There might be more to be done, but
> > I
> > > > don't
> > > > think we could gain anything really substantial.
> > >
> > > probably we have been down this road before but is another option
> > to 
> > > pre-compile and distribute the Windows binaries?
> > >
> > > Martin
> > >
> > > >
> > > > Laurent
> > > >
> > > > > jo
> > > > >
> > > > > > Martin
> > > > > >
> > > > > > > On linux and macOS all is fine, but we get TIMEOUT errors
> > on
> > > > > > > a regular basis on Windows (I guess because it has to be
> > > > > > > compiled for i386 and x86_64). The problem is that a
> > failing
> > > > > > > mzR causes all packages depending on it (like MSnbase and
> > > > > > > xcms) to fail too.
> > > > > > > cheers, jo
> > > > > > > ___
> > > > > > > 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.
> > > > >
> > > > > ___
> > > > > Bioc-devel@r-project.org mailing list
> > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > >
> > > >
> > >
> > >
> > > This email message may contain legally privileged
> > > and/or...{{dropped:2}}
> > >
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > --
> > 
>