Re: [Bioc-devel] rtracklayer::import.bed(genome = Seqinfo)
Hi Aditya,
This is probably best asked on the support site. When you post there,
please include your sessionInfo().
Thanks,
Michael
On Tue, Oct 22, 2019 at 9:50 AM Bhagwat, Aditya
wrote:
>
> Dear Michael,
>
> Sorry for my incomplete email - the send button got hit too fast. Better this
> time.
>
> rtracklayer::import.bed mentions the argument "genome" to be either a genome
> identifier (like 'mm10') or a Seqinfo object.
>
> I notice that the second option does not work on my BED file (in attach).
>
> # This works
> rtracklayer::import.bed('SRF.bed', genome = 'mm10') # this works
>
> # But this doesn't
> seqinfo1<-
> GenomeInfoDb::seqinfo(BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10)
> rtracklayer::import.bed('SRF.bed', genome = seqinfo1)
>
> So I am requesting feedback.
> I thought to use this channel
>
> Aditya
--
Michael Lawrence
Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
micha...@gene.com
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Re: [Bioc-devel] ndexr fails on vignette build on windows
May I ask what is the resolution here? I have updated curl and httr on my
windows box and continue
to see errors unique to windows when requests lack the protocol in the URL.
On Wed, Oct 23, 2019 at 7:28 AM Shepherd, Lori <
lori.sheph...@roswellpark.org> wrote:
> Thank you for the update.
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
> From: Florian J. Auer
> Sent: Wednesday, October 23, 2019 7:25 AM
> To: Shepherd, Lori ;
> bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] ndexr fails on vignette build on windows
>
>
> Hi Lori,
>
> Thanks a lot, that really helped!
>
> It seems, that the error is caused by httr, and curl in the end.
>
>
> https://github.com/r-lib/httr/issues/619
>
>
> Greetings
>
> Florian
>
>
>
> Am 09.10.19 um 17:37 schrieb Shepherd, Lori:
> I did a little digging and here is what I've found...
>
>
> I R CMD Stangle the vignette and then sourced the code:
>
>
> > source("ndexr-vignette.R", echo=TRUE)
>
> > ##
> eval=FALSE-
> > ## if (!requireNamespace("BiocManager", quietly=TRUE))
> > ## instal [TRUNCATED]
>
> > ##
> eval=FALSE-
> > ## ## login to the NDEx server
> > ## ndexcon = ndex_connect("username", [TRUNCATED]
> Error in if (is_http) { : argument is of length zero
> > traceback()
> 8: request_perform(req, hu$handle$handle)
> 7: httr::GET(url = url, config = auth_param) at ndex_helper.r#149
> 6: ndex_helper_httpResponseHandler(httr::GET(url = url, config =
> auth_param),
>log_txt, verbose) at ndex_connect.r#84
> 5: ndex_connect() at ndexr-vignette.R#24
> 4: eval(ei, envir)
> 3: eval(ei, envir)
> 2: withVisible(eval(ei, envir))
> 1: source("ndexr-vignette.R", echo = TRUE)
>
>
> If I then did a
> debug(httr:::request_perform)
>
> httr:::request_fetch results in different output on windows than on
> mac/linux
>
>
>
> #
> # on linux and mac
> #
>
> Browse[2]> resp
> $url
> [1] "HTTP://www.ndexbio.org/v2/admin/status"<
> HTTP://www.ndexbio.org/v2/admin/status>
>
>
> #
> # on windows
> #
>
> Browse[2]> resp
> $url
> [1] "www.ndexbio.org/v2/admin/status<
> http://www.ndexbio.org/v2/admin/status>"
>
> This causes the eventual error.
>
>
> You might try to come up with a small reproducible example and report as a
> bug to httr.
>
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
>
> From: Bioc-devel bioc-devel-boun...@r-project.org> on behalf of Florian J. Auer <
> florian.a...@informatik.uni-augsburg.de> florian.a...@informatik.uni-augsburg.de>
> Sent: Thursday, September 26, 2019 7:52 AM
> To: bioc-devel@r-project.org <
> bioc-devel@r-project.org>
> Subject: [Bioc-devel] ndexr fails on vignette build on windows
>
> Hi everyone,
>
> my package ndexr produces some errors while building the vignette, but
> only in the Windows build.
>
> In particular, the error message shows:
>
> Quitting from lines 76-78 (ndexr-vignette.Rmd)
> Error: processing vignette 'ndexr-vignette.Rmd' failed with diagnostics:
> argument is of length zero
> --- failed re-building 'ndexr-vignette.Rmd'
>
> Seems like it's occurring in the following lines:
>
> ```{r, echo=FALSE, results='hide', message=FALSE}
> ## login to the NDEx server
> ndexcon = ndex_connect()
> ```
>
> Is there some different behavior in Windows of how the code blocks are
> treated? Or is the error occurring within the code?
>
> Have there been some changes on the build server, since the error only
> occurred recently without any changes in the package?
>
> I'm grateful for any feedback!
>
> Greetings
>
> Florian
>
> --
> Dipl.Bioinf. Florian Auer
> IT Infrastructure for Translational Medical Research
> Faculty of Applied Computer Science
> Faculty of Medicine
> University of Augsburg
> Alter Postweg 101
> 86159 Augsburg
>
> email: florian.a...@informatik.uni-augsburg.de florian.a...@informatik.uni-augsburg.de>
> phone: (+49) 0821- 598 - 3748
>
>
> [[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
Re: [Bioc-devel] pwrEWAS package: Error in CHECK during checkResults on Windows
Hi Stefan,
It looks like a connectivity issue, likely a transient one. I would just
wait and see if it goes away in the next days.
Thanks for keeping a close eye on the build results for your package.
Best,
H.
On 10/23/19 11:20, Graw, Stefan H wrote:
> Dear devel team,
>
> My package "pwrEWAS" produced an error (see below) during checkResults in
> CHECK on the windows server. I previously had an OK and did not change
> anything. Should I just wait for the next build or how can I fix this issue?
>
> Thanks,
> Stefan
>
>
>
> ** running examples for arch 'x64' ... ERROR
> Running examples in 'pwrEWAS-Ex.R' failed
> The error most likely occurred in:
>
>> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
>> ### Name: pwrEWAS
>> ### Title: pwrEWAS - A computationally efficient tool for comprehensive
>> ### power estimation in EWAS
>> ### Aliases: pwrEWAS
>> ### Keywords: DNAm microarray power
>>
>> ### ** Examples
>>
>> outDelta <- pwrEWAS(minTotSampleSize = 10,
> + maxTotSampleSize = 20,
> + SampleSizeSteps = 10,
> + NcntPer = 0.5,
> + targetDelta = c(0.2, 0.5),
> + J = 1000,
> + targetDmCpGs = 10,
> + tissueType = "Adult (PBMC)",
> + detectionLimit = 0.01,
> + DMmethod = "limma",
> + FDRcritVal = 0.05,
> + core = 2,
> + sims = 30)
> Using temporary cache
> C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpIhL8JZ/BiocFileCache
> Warning: download failed
>web resource path:
> 'https://urldefense.proofpoint.com/v2/url?u=https-3A__experimenthub.bioconductor.org_metadata_experimenthub.sqlite3=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=4IVJ68WGWUI9QgCUkQl_JPz4iddilcl4o3MlQ7Tfkqw=dwyzUba3xBdIO4kUqbc_AcBCsbI4oX3-0_mn46VpJ84=
> '
>local file path:
> 'C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpIhL8JZ/BiocFileCache/1e987801b42_experimenthub.sqlite3'
>reason: Timeout was reached: [experimenthub.bioconductor.org] Connection
> timed out after 10014 milliseconds
> Warning: bfcadd() failed; resource removed
>rid: BFC1
>fpath:
> 'https://urldefense.proofpoint.com/v2/url?u=https-3A__experimenthub.bioconductor.org_metadata_experimenthub.sqlite3=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=4IVJ68WGWUI9QgCUkQl_JPz4iddilcl4o3MlQ7Tfkqw=dwyzUba3xBdIO4kUqbc_AcBCsbI4oX3-0_mn46VpJ84=
> '
>reason: download failed
> Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) :
>bfcadd() failed; see warnings()
> Calls: pwrEWAS ... .create_cache -> .updateHubDB -> bfcadd -> bfcadd ->
> .util_download
> Execution halted
>
>
> From
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.10_bioc-2DLATEST_pwrEWAS_tokay1-2Dchecksrc.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=4IVJ68WGWUI9QgCUkQl_JPz4iddilcl4o3MlQ7Tfkqw=OLr1C0h-Ctwe-4W21Dp_kNsWRD_yoM0ro64ZTsVKgAQ=
>
> --
> Confidentiality Notice: This e-mail message, including a...{{dropped:10}}
>
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=4IVJ68WGWUI9QgCUkQl_JPz4iddilcl4o3MlQ7Tfkqw=HCvWI2DfbulgAzBW_rfLYGdoi949sMtmDlO00JAqSvQ=
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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[Bioc-devel] pwrEWAS package: Error in CHECK during checkResults on Windows
Dear devel team,
My package "pwrEWAS" produced an error (see below) during checkResults in CHECK
on the windows server. I previously had an OK and did not change anything.
Should I just wait for the next build or how can I fix this issue?
Thanks,
Stefan
** running examples for arch 'x64' ... ERROR
Running examples in 'pwrEWAS-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pwrEWAS
> ### Title: pwrEWAS - A computationally efficient tool for comprehensive
> ### power estimation in EWAS
> ### Aliases: pwrEWAS
> ### Keywords: DNAm microarray power
>
> ### ** Examples
>
> outDelta <- pwrEWAS(minTotSampleSize = 10,
+ maxTotSampleSize = 20,
+ SampleSizeSteps = 10,
+ NcntPer = 0.5,
+ targetDelta = c(0.2, 0.5),
+ J = 1000,
+ targetDmCpGs = 10,
+ tissueType = "Adult (PBMC)",
+ detectionLimit = 0.01,
+ DMmethod = "limma",
+ FDRcritVal = 0.05,
+ core = 2,
+ sims = 30)
Using temporary cache
C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpIhL8JZ/BiocFileCache
Warning: download failed
web resource path:
'https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3'
local file path:
'C:\Users\biocbuild\bbs-3.10-bioc\tmpdir\RtmpIhL8JZ/BiocFileCache/1e987801b42_experimenthub.sqlite3'
reason: Timeout was reached: [experimenthub.bioconductor.org] Connection
timed out after 10014 milliseconds
Warning: bfcadd() failed; resource removed
rid: BFC1
fpath: 'https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3'
reason: download failed
Error in .util_download(x, rid[i], proxy, config, "bfcadd()", ...) :
bfcadd() failed; see warnings()
Calls: pwrEWAS ... .create_cache -> .updateHubDB -> bfcadd -> bfcadd ->
.util_download
Execution halted
>From
>https://bioconductor.org/checkResults/3.10/bioc-LATEST/pwrEWAS/tokay1-checksrc.html
--
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Re: [Bioc-devel] HDF5Array/DelayedArray matrix operations fail on windows
Hi Kevin, Running this particular code (e.g. the code in the test-sparsematrix.R file) also works for me on our Windows builders. However, trying to run the **full suite** of tests does trigger the error. So it seems to be a situation where some code in some other tests is altering the state of the session in a way that breaks the `scMerge()` calls in test-hdf5array.R and test-sparsematrix.R. I see that you use parallelization a lot. Could it be that some code at some point alters the state of the current parallelization backend? All these socketConnection() warnings makes me suspect that. This would also explain why we only see the problem on Windows. Parallelization problems are very platform specific and tend to occur more often on Windows where backends like MulticoreParam are not supported. Best, H. On 10/21/19 23:32, Kevin Wang wrote: > Hi, I am trying to make my package scMerge to be compatible with HDF5Array. > While all the checks passed on Linux and Mac, it errored on Windows > (https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_3.10_bioc-2DLATEST_scMerge_=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Id_OfFGj844t8jvq9xPxtMaF-nCPVZ5EtPR5nv0Hiwk=wQziv6_QxHSybX-rtoi3C555HFUVEY19GZ44tKr3knA= > ). Upon closer inspection, the failures seem to come a test for > compatibility of HDF5Array > (the script can be viewed here > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_SydneyBioX_scMerge_blob_master_tests_testthat_test-2Dhdf5array.R=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Id_OfFGj844t8jvq9xPxtMaF-nCPVZ5EtPR5nv0Hiwk=MWdFZy6IM1p7JLqe93W5_OG0D4kf79BIJm12U2BDS78= > ). The error message was "non-numeric argument to binary operator” and calls > to DelayedArray. I have tried to run this specific line on a Windows machine > with Rtools35 installed and there was no error. A similar scenario occurred > for sparse matrix > (https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_SydneyBioX_scMerge_blob_master_tests_testthat_test-2Dsparsematrix.R=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Id_OfFGj844t8jvq9xPxtMaF-nCPVZ5EtPR5nv0Hiwk=ACuxhvv3ZHIB1CXLN0gvFo7LDQmOnaeipbdnstyDdZo= > ) where the error was "'a' must be a numeric matrix”. > > Any help is greatly appreciated. > > Thank you > Best Wishes > Kevin > The University of Sydney > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Id_OfFGj844t8jvq9xPxtMaF-nCPVZ5EtPR5nv0Hiwk=y023axwxFTrmasaeZ5wAbdc_6HYpjglnD9fb3Jt4gyM= > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] ndexr fails on vignette build on windows
Thank you for the update.
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Florian J. Auer
Sent: Wednesday, October 23, 2019 7:25 AM
To: Shepherd, Lori ; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] ndexr fails on vignette build on windows
Hi Lori,
Thanks a lot, that really helped!
It seems, that the error is caused by httr, and curl in the end.
https://github.com/r-lib/httr/issues/619
Greetings
Florian
Am 09.10.19 um 17:37 schrieb Shepherd, Lori:
I did a little digging and here is what I've found...
I R CMD Stangle the vignette and then sourced the code:
> source("ndexr-vignette.R", echo=TRUE)
> ## eval=FALSE-
> ## if (!requireNamespace("BiocManager", quietly=TRUE))
> ## instal [TRUNCATED]
> ## eval=FALSE-
> ## ## login to the NDEx server
> ## ndexcon = ndex_connect("username", [TRUNCATED]
Error in if (is_http) { : argument is of length zero
> traceback()
8: request_perform(req, hu$handle$handle)
7: httr::GET(url = url, config = auth_param) at ndex_helper.r#149
6: ndex_helper_httpResponseHandler(httr::GET(url = url, config = auth_param),
log_txt, verbose) at ndex_connect.r#84
5: ndex_connect() at ndexr-vignette.R#24
4: eval(ei, envir)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source("ndexr-vignette.R", echo = TRUE)
If I then did a
debug(httr:::request_perform)
httr:::request_fetch results in different output on windows than on mac/linux
#
# on linux and mac
#
Browse[2]> resp
$url
[1]
"HTTP://www.ndexbio.org/v2/admin/status"
#
# on windows
#
Browse[2]> resp
$url
[1] "www.ndexbio.org/v2/admin/status"
This causes the eventual error.
You might try to come up with a small reproducible example and report as a bug
to httr.
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 Florian J. Auer
Sent: Thursday, September 26, 2019 7:52 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] ndexr fails on vignette build on windows
Hi everyone,
my package ndexr produces some errors while building the vignette, but
only in the Windows build.
In particular, the error message shows:
Quitting from lines 76-78 (ndexr-vignette.Rmd)
Error: processing vignette 'ndexr-vignette.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'ndexr-vignette.Rmd'
Seems like it's occurring in the following lines:
```{r, echo=FALSE, results='hide', message=FALSE}
## login to the NDEx server
ndexcon = ndex_connect()
```
Is there some different behavior in Windows of how the code blocks are
treated? Or is the error occurring within the code?
Have there been some changes on the build server, since the error only
occurred recently without any changes in the package?
I'm grateful for any feedback!
Greetings
Florian
--
Dipl.Bioinf. Florian Auer
IT Infrastructure for Translational Medical Research
Faculty of Applied Computer Science
Faculty of Medicine
University of Augsburg
Alter Postweg 101
86159 Augsburg
email:
florian.a...@informatik.uni-augsburg.de
phone: (+49) 0821- 598 - 3748
[[alternative HTML version deleted]]
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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.
--
Dipl.Bioinf. Florian Auer
IT Infrastructure for Translational Medical Research
Faculty of Applied Computer Science
Faculty of Medicine
University of Augsburg
Alter Postweg 101
86159 Augsburg
email:
florian.a...@informatik.uni-augsburg.de
phone: (+49) 0821- 598 - 3748
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),
Re: [Bioc-devel] ndexr fails on vignette build on windows
Hi Lori,
Thanks a lot, that really helped!
It seems, that the error is caused by httr, and curl in the end.
https://github.com/r-lib/httr/issues/619
Greetings
Florian
Am 09.10.19 um 17:37 schrieb Shepherd, Lori:
> I did a little digging and here is what I've found...�
>
>
> I R CMD Stangle the vignette and then sourced the code:
>
>
> > source("ndexr-vignette.R", echo=TRUE)
>
> > ##
> eval=FALSE-
> > ## if (!requireNamespace("BiocManager", quietly=TRUE))
> > ## � � instal [TRUNCATED]
>
> > ##
> eval=FALSE-
> > ## ## login to the NDEx server
> > ## ndexcon = ndex_connect("username", [TRUNCATED]
> Error in if (is_http) { : argument is of length zero
> > traceback()
> 8: request_perform(req, hu$handle$handle)
> 7: httr::GET(url = url, config = auth_param) at ndex_helper.r#149
> 6: ndex_helper_httpResponseHandler(httr::GET(url = url, config =
> auth_param),
> � � � �log_txt, verbose) at ndex_connect.r#84
> 5: ndex_connect() at ndexr-vignette.R#24
> 4: eval(ei, envir)
> 3: eval(ei, envir)
> 2: withVisible(eval(ei, envir))
> 1: source("ndexr-vignette.R", echo = TRUE)
>
>
> If I then did a�
> debug(httr:::request_perform)�
>
> httr:::request_fetch results in different output on windows than on
> mac/linux
>
>
>
> #
> # on linux and mac
> #
>
> Browse[2]> resp
> $url
> [1] "HTTP://www.ndexbio.org/v2/admin/status"
>
>
> #
> # on windows
> #
>
> Browse[2]> resp
> $url
> [1] "www.ndexbio.org/v2/admin/status"
>
> This causes the eventual error.��
>
>
> You might try to come up with a small reproducible example and report
> as a bug to httr.�
>
>
>
> 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
> Florian J. Auer
> *Sent:* Thursday, September 26, 2019 7:52 AM
> *To:* bioc-devel@r-project.org
> *Subject:* [Bioc-devel] ndexr fails on vignette build on windows
> �
> Hi everyone,
>
> my package ndexr produces some errors while building the vignette, but
> only in the Windows build.
>
> In particular, the error message shows:
>
> Quitting from lines 76-78 (ndexr-vignette.Rmd)
> Error: processing vignette 'ndexr-vignette.Rmd' failed with diagnostics:
> argument is of length zero
> --- failed re-building 'ndexr-vignette.Rmd'
>
> Seems like it's occurring in the following lines:
>
> ```{r, echo=FALSE, results='hide', message=FALSE}
> ## login to the NDEx server
> ndexcon = ndex_connect()
> ```
>
> Is there some different behavior in Windows of how the code blocks are
> treated? Or is the error occurring within the code?
>
> Have there been some changes on the build server, since the error only
> occurred recently without any changes in the package?
>
> I'm grateful for any feedback!
>
> Greetings
>
> Florian
>
> --
> Dipl.Bioinf. Florian Auer
> IT Infrastructure for Translational Medical Research
> Faculty of Applied Computer Science
> Faculty of Medicine
> University of Augsburg
> Alter Postweg 101
> 86159 Augsburg
>
> email: florian.a...@informatik.uni-augsburg.de
> phone: (+49) 0821- 598 - 3748
>
>
> ��� [[alternative HTML version deleted]]
>
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--
Dipl.Bioinf. Florian Auer
IT Infrastructure for Translational Medical Research
Faculty of Applied Computer Science
Faculty of Medicine
University of Augsburg
Alter Postweg 101
86159 Augsburg
email: florian.a...@informatik.uni-augsburg.de
phone: (+49) 0821- 598 - 3748
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