Re: [Bioc-devel] CNORfeeder building error

2020-04-02 Thread Shepherd, Lori
When I look at the git.bioconductor.org checkout of your package,

There are no R functions and no man functions for those exports.

Your commit on Mar 30 only updated the NAMESPACE and vignette.



base) lori@lori-HP-ZBook-15-G2:~/b/Rpacks/CNORfeeder(master)$ grep -r 
"buildFeederObjectDynamic" *
NAMESPACE:"buildFeederObjectDynamic",
vignettes/CNORfeeder-vignette.Rnw:feederObject = buildFeederObjectDynamic(model 
= model, cnolist = cnolist,


Please check your commits.  You may have forgotten to git add the relevant 
files.




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 Enio Gjerga 

Sent: Thursday, April 2, 2020 3:54 PM
To: Herv� Pag�s 
Subject: [Bioc-devel] CNORfeeder building error

Hello,

I am the maintainer of the CNORfeeder package. When I updated the package I
added a few other functions. However, from the building I get the following
error:

package ornamespace load failed for �CNORfeeder� in
namespaceExport(ns, exports):
undefinedexports: *the names of the new functions I have added*

I have added these function names on the NAMESPACE as exports and also they
are in the /man function documentation (as .Rd files) and of course as R
functions in /R.

Please, what might be the reason for this? Should these new functions also
be declared somewhere else which I am missing?

I have run the 'R CMD INSTALL CNORfeeder' command in my terminal and the
package seem to be built just fine. I am using Mac OS X El Captain.

Best,
Enio
--
Enio GJERGA
PhD student
JRC-COMBINE RWTH Aachen
Tel : +4917685132057

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[Bioc-devel] CNORfeeder building error

2020-04-02 Thread Enio Gjerga
Hello,

I am the maintainer of the CNORfeeder package. When I updated the package I
added a few other functions. However, from the building I get the following
error:

package ornamespace load failed for ‘CNORfeeder’ in
namespaceExport(ns, exports):
undefinedexports: *the names of the new functions I have added*

I have added these function names on the NAMESPACE as exports and also they
are in the /man function documentation (as .Rd files) and of course as R
functions in /R.

Please, what might be the reason for this? Should these new functions also
be declared somewhere else which I am missing?

I have run the 'R CMD INSTALL CNORfeeder' command in my terminal and the
package seem to be built just fine. I am using Mac OS X El Captain.

Best,
Enio
-- 
Enio GJERGA
PhD student
JRC-COMBINE RWTH Aachen
Tel : +4917685132057

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Re: [Bioc-devel] Development branch build error from celda

2020-04-02 Thread Shepherd, Lori
I think this is an intermittent connectivity issue and is safe to ignore. While 
today's build report has not yet officially posted, I check the report for you 
package and it seems to be all OK.
Thank you for your diligence on investigating package ERRORs.

Cheers,


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 Wang, Zhe 

Sent: Thursday, April 2, 2020 1:46 AM
To: Bioc-devel@r-project.org 
Subject: [Bioc-devel] Development branch build error from celda

Hi,

I am the maintainer of Bioconductor package celda. Recently there is an build 
check error on the development branch specifically on Windows i386 platform. I 
cannot reproduce this error on my local x64 Windows machine. The error report 
is as follows:

* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'celda-Ex.R' failed
Warning in file(con, "r") :
  cannot open file '../celda-Ex_i386.Rout': Permission denied
Error in file(con, "r") : cannot open the connection
Execution halted

Does anyone have any idea about how I can fix this?

Thanks,
Zhe

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Re: [Bioc-devel] Help with tokay2 errors

2020-04-02 Thread Shepherd, Lori
On quick glance into the logs on tokay2 it looks like it may be an issue with 
MotifDb and not your package.
In merge_motif it doesn't get to evaluating the code as it is hung up on trying 
to load the MotifDb library.  Once this library is called,
There are numerous:

*** recursive gc invocation

and somewhere in the middle of all these repeated lines is

Error: package or namespace load failed for 'MotifDb':
 .onLoad failed in loadNamespace() for 'MotifDb', details:
  call: base::colSums(x, na.rm = na.rm, dims = dims, ...)
  error: bad binding access
Execution halted




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 Benjamin 
Jean-Marie Tremblay 
Sent: Saturday, March 28, 2020 4:22 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Help with tokay2 errors

Hi,

Recently I've been having several examples fail on the tokay2 test machine,
specifically the i386 examples. Unfortunately I don't have access to a
windows machine to diagnose these failures right now, and the output that I
can see shows no errors; the examples just end abruptly. I don't see these
failures on my own computer (regular macOS, also docker bioc-devel image), so
I�m at a bit of a loss as to how to go about fixing these.

http://bioconductor.org/checkResults/devel/bioc-LATEST/universalmotif/tokay2-checksrc.html

Any help would be greatly appreciated.

Thanks,

Benjamin Tremblay
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Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.11

2020-04-02 Thread Shepherd, Lori


Software package: DChIPRep

and

Workflow package: maEndToEnd

User requested deprecation.




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Shepherd, Lori
Sent: Monday, March 30, 2020 11:36 AM
To: bioc-devel@r-project.org 
Subject: Final List of Deprecated Packages for Bioc3.11

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 list will be updated monthly. This is the current list 
of deprecated packages for Bioc 3.11 :

Maintainer requested deprecation:

Software:

QUALIFIER
motifRG
triform
CVE
proteoQC
affypdnn
splicegear
Genominator
IdMappingAnalysis
IdMappingRetrieval
manta
RefNet
AnalysisPageServer
scfind
kimod
plw
cn.mops
cobindR
LMGene
sRAP
gCMAP
gCMAPWeb
DESeq


Annotation:

org.At.tair.db
hom.At.inp.db
hom.Ce.inp.db
hom.Dm.inp.db
hom.Dr.inp.db
hom.Hs.inp.db
hom.Mm.inp.db
hom.Rn.inp.db
hom.Sc.inp.db
KEGG.db (use KEGGREST instead)


Unresponsive/not-maintained packages:

Software:

SELEX
CTDquerier
MTseeker
readat
anamiR
MEAL
BiSeq
CALIB
cellGrowth
chroGPS
DEDS
LVSmiRNA
MANOR
MCRestimate
nem
PAPi
pcaGoPromoter
pint
RIPSeeker
SANTA
waveTiling
BayesPeak
bgafun
lol
M3D
MergeMaid
IPPD
biosvd
birta
DupChecker
FEM
geecc
MaxContrastProjection
mitoODE
MoPS
PowerExplorer
Vega


ExpermentData:

MTseekerData
RIPSeekerData


The follow Annotation packages were deprecated in 3.10 and removed from 3.11 
but not previously announced.

MafDb.ESP6500SI.V2.SSA137.hs37d5
MafDb.EXP6500SI.V2.SSA137.GRCh38

It should be noted, we did try to reach out to these package maintainers 
multiple times and they were either unresponsive or had emails bounce. We 
encourage anyone that is familiar with a package maintainer on this list to 
reach out to them and notify them directly. Packages can be un-deprecated if a 
maintainer fixes the package to build/check cleanly before the next release and 
requests un-deprecation on the bioc-devel@r-project.org mailing list.

We will be sending 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.

We will still be keeping track of failing packages and compiling a list to 
deprecate immediately after the release. This could have been because the 
package has reverse dependencies or was identified to late to deprecate in 
3.11. We encourage anyone that knows the maintainers of these packages to reach 
out to them to fix their package to avoid deprecation. The current list for 
immediate deprecation in 3.12 is:

DESeq
MotIV
NOISeq
omicade4
PGSEA
Starr
VanillaICE


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 
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Re: [Bioc-devel] Unable to update maintainer email address

2020-04-02 Thread Turaga, Nitesh
Hi,

I've updated your email address to the one you are emailing from now. 
pierre.neuv...@math.cnrs.fr.

Please "activate" you BiocCredentials account first and add SSH keys. Once you 
do that you'll be able to change the email on the description file. 

https://git.bioconductor.org/BiocCredentials/account_activation/

Best,

Nitesh 

> On Apr 2, 2020, at 7:22 AM, Pierre Neuvial  
> wrote:
> 
> Hello,
> 
> I am the maintainer of the MANOR package. This package is listed in
> "Unresponsive/not-maintained packages:" because I did not update my email
> after moving to my current position, and this email does not exist anymore.
> 
> I understand that I need to update the email in the DESCRIPTION of the
> MANOR package with the one I am writing with. However, I don't think I can
> do this because I do not have an active BiocCrendentials account yet,
> and... I can't activate my BiocCredentials account, since the email
> associated with the package is not working anymore.
> 
> If this is the correct way to go, can a BioC admin update my email in the
> DESCRIPTION of the MANOR package with the one I am writing with in order to
> break this circle?
> 
> All the best,
> 
> Pierre
> 
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> 
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Re: [Bioc-devel] Problems with Biocredentials

2020-04-02 Thread Turaga, Nitesh
Yes, that is the problem. I'm not sure how you have two accounts for two 
packages. It might be because you submitted both packages with different email 
addresses as maintainer, one from a "Perkins" account and the other from "wehi" 
account.

I've fixed the issue. Please try again, and see that you have access to all 
your packages.

Best,

Nitesh 

> On Apr 1, 2020, at 9:04 AM, Turaga, Nitesh  
> wrote:
> 
> Hi, 
> 
> Did you add your Github username to your BiocCredentials account? 
> 
> If you add your Github username to your BiocCredentials account, it will 
> import the SSH keys you add on your Github account.
> 
> Best,
> 
> Nitesh 
> 
>> On Mar 31, 2020, at 11:46 PM, Saskia Freytag  wrote:
>> 
>> Hi,
>> 
>> I have added an SSH key to my GitHub and to the Biocredentials app, but I 
>> still cannot see my GitHub username appear. I think that my GitHub Username 
>> is also registered to another email and package (schex), could this lead to 
>> problems?
>> 
>> Cheers,
>> 
>> Saskia
>> ___
>> 
>> The information in this email is confidential and =\ i...{{dropped:17}}
> 
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[Bioc-devel] Unable to update maintainer email address

2020-04-02 Thread Pierre Neuvial
Hello,

I am the maintainer of the MANOR package. This package is listed in
"Unresponsive/not-maintained packages:" because I did not update my email
after moving to my current position, and this email does not exist anymore.

I understand that I need to update the email in the DESCRIPTION of the
MANOR package with the one I am writing with. However, I don't think I can
do this because I do not have an active BiocCrendentials account yet,
and... I can't activate my BiocCredentials account, since the email
associated with the package is not working anymore.

If this is the correct way to go, can a BioC admin update my email in the
DESCRIPTION of the MANOR package with the one I am writing with in order to
break this circle?

All the best,

Pierre

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