Re: [Bioc-devel] EXTERNAL: "invalid connection" when building vignette - Windows only

[Ramos Perez, Marcel via Bioc-devel]

Hi Matteo,

You can get the traceback by running

 rmarkdown::render("vignettes/Moonlight2R.Rmd")


Best regards,

Marcel


On 3/18/24 4:54 AM, Matteo Tiberti wrote:
> Hi Ramos,
> 
> Thank you very much – this is really informative. Can I ask you how you 
> got the tracback? I’m not really used at debugging this sort of issues.
> 
> I can see that the EpiMix::EpiMix function we use does use foreach 
> (foreach::makeCluster and %dopar%). I have no experience with foreach, 
> but I had a dig, and I can see that this function cleans up the parallel 
> environment with stopCluster only before just one of the several returns 
> it has. So it is possible that the environment isn’t cleaned up between 
> consequent function calls. We will investigate.
> 
> Of course if anyone with more foreach experience wants to pinch in, they 
> are very welcome
> 
> Thank you again
> 
> 
> Matteo Tiberti
> 
> *Danish Cancer Institute*
> Strandboulevarden 49
> DK-2100 Copenhagen
> *Telephone*: +45 35 25 73 07
> /– a part of the Danish Cancer Society/
> 
> An image showing the Danish Cancer Society's name and logo called the 
> bow in red font. Displayed in red 
> 
> 
> www.cancer.dk 
> 
>  | Our privacy policy 
> 
> 
> *From: *Ramos Perez, Marcel 
> *Date: *Friday, 15 March 2024 at 22.44
> *To: *bioc-devel@r-project.org 
> *Cc: *Matteo Tiberti 
> *Subject: *Re: EXTERNAL: [Bioc-devel] "invalid connection" when building 
> vignette - Windows only
> 
> Hi Matteo,
> 
> I was also able to reproduce on Bioc 3.18 on Windows with a traceback 
> (see below).
> 
> It may be that there are symbol clashes between parallel runs in the
> `foreach:::.foreachGlobals` environment as described in
> https://stackoverflow.com/a/67497500 
> 
> 
> Clearing the symbols in that environment alleviates the problem temporarily
> until running the chunk in line 1124 where the same error occurs.
> 
> Someone with more experience using `foreach` and socket clusters may be 
> able to help.
> 
> Note that the code should be running on either one or two cores by default.
> 
> Best regards,
> 
> Marcel
> 
> ```
> 
> processing file: Moonlight2R.Rmd
>    |...    |  45% 
> [unnamed-chunk-20]
> Quitting from lines 727-746 [unnamed-chunk-20] (Moonlight2R.Rmd)
> 
> Error in `summary.connection()`:
> ! invalid connection
> Backtrace:
>    1. Moonlight2R::GMA(...)
>    2. EpiMix::EpiMix(...)
>     at Moonlight2R/R/GMA.R:117:3
>    3. EpiMix:::MethylMix_MixtureModel(...)
>    4. ... %dopar% ...
>   ...
>    7. parallel:::sendCall(cl[[i]], fun, list(...))
>    8. parallel:::postNode(...)
>   10. parallel:::sendData.SOCKnode(...)
>   11. base::serialize(data, node$con)
>   13. base::summary.connection(connection)
> Execution halted
> 
> ```
> 
> On 3/15/24 6:05 AM, Matteo Tiberti via Bioc-devel wrote:
> 
> Dear developers,
> 
> we've been getting a build fail for our Moonlight2R package on
> Windows only, during vignette build in CHECK, which just prints out
> an "invalid connection" error:
> 
> Quitting from lines 727-746 [unnamed-chunk-20] (Moonlight2R.Rmd)
> Error: processing vignette 'Moonlight2R.Rmd' failed with diagnostics:
> invalid connection
> --- failed re-building 'Moonlight2R.Rmd'
> 
> The 

Re: [Bioc-devel] EXTERNAL: "invalid connection" when building vignette - Windows only

[Ramos Perez, Marcel via Bioc-devel]

Hi Matteo,

I was also able to reproduce on Bioc 3.18 on Windows with a traceback (see 
below).

It may be that there are symbol clashes between parallel runs in the
`foreach:::.foreachGlobals` environment as described in
https://stackoverflow.com/a/67497500

Clearing the symbols in that environment alleviates the problem temporarily
until running the chunk in line 1124 where the same error occurs.

Someone with more experience using `foreach` and socket clusters may be able to 
help.

Note that the code should be running on either one or two cores by default.

Best regards,

Marcel

```

processing file: Moonlight2R.Rmd
  |...|  45% [unnamed-chunk-20]
Quitting from lines 727-746 [unnamed-chunk-20] (Moonlight2R.Rmd)

Error in `summary.connection()`:
! invalid connection
Backtrace:
  1. Moonlight2R::GMA(...)
  2. EpiMix::EpiMix(...)
   at Moonlight2R/R/GMA.R:117:3
  3. EpiMix:::MethylMix_MixtureModel(...)
  4. ... %dopar% ...
 ...
  7. parallel:::sendCall(cl[[i]], fun, list(...))
  8. parallel:::postNode(...)
 10. parallel:::sendData.SOCKnode(...)
 11. base::serialize(data, node$con)
 13. base::summary.connection(connection)
Execution halted

```

On 3/15/24 6:05 AM, Matteo Tiberti via Bioc-devel wrote:
Dear developers,

we've been getting a build fail for our Moonlight2R package on Windows only, 
during vignette build in CHECK, which just prints out an "invalid connection" 
error:

Quitting from lines 727-746 [unnamed-chunk-20] (Moonlight2R.Rmd)
Error: processing vignette 'Moonlight2R.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'Moonlight2R.Rmd'

The following snippet is the code chunk that causes the fail:

data("dataMethyl")
data("dataFilt")
data("dataPRA")
data("DEGsmatrix")
data("LUAD_sample_anno")
data("NCG")
data("EncodePromoters")
data("MetEvidenceDriver")

# Subset column names (sample names) in expression data to patient level
pattern <- "^(.{4}-.{2}-.{4}-.{2}).*"
colnames(dataFilt) <- sub(pattern, "\\1", colnames(dataFilt))

dataGMA <- GMA(dataMET = dataMethyl, dataEXP = dataFilt,
  dataPRA = dataPRA, dataDEGs = DEGsmatrix,
  sample_info = LUAD_sample_anno, met_platform = "HM450",
  prevalence_filter = NULL,
  output_dir = "./GMAresults", cores = 1, roadmap.epigenome.ids = 
"E096",
  roadmap.epigenome.groups = NULL)

I could reproduce this fail on my local Windows machine (on release rather than 
devel at the moment), so it's probably not an issue with the builders. It 
builds and runs successfully on Linux, both on devel and release. I have also 
tried running the same code by hand on the R prompt, and that completes 
successfully.

The error I get when trying to build the vignette manually is possibly more 
informative:


devtools::build_vignettes('../Downloads/Moonlight2R-devel/Moonlight2R-devel/')

ℹ Installing Moonlight2R in temporary library
ℹ Building vignettes for Moonlight2R
--- re-building 'Moonlight2R.Rmd' using rmarkdown

processing file: Moonlight2R.Rmd
 |...|  45% 
[unnamed-chunk-20]trying URL 
'https://bioconductor.org/packages/3.18/data/experiment/src/contrib/sesameData_1.20.0.tar.gz'



trying URL 
'https://bioconductor.org/packages/3.18/data/experiment/src/contrib/sesameData_1.20.0.tar.gz'
Content type 'application/x-gzip' length 1975798 bytes (1.9 MB)
==
downloaded 1.9 MB

* installing *source* package 'sesameData' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading

** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location


** testing if installed package can be loaded from final location



** testing if installed package keeps a record of temporary installation path
* DONE (sesameData)

The downloaded source packages are in
   'C:\Users\Work\AppData\Local\Temp\RtmpmsVLSL\downloaded_packages'

Quitting from lines 727-746 [unnamed-chunk-20] (Moonlight2R.Rmd)

Error: processing vignette 'Moonlight2R.Rmd' failed with diagnostics:
invalid connection
--- failed re-building 'Moonlight2R.Rmd'

SUMMARY: processing the following file failed:
 'Moonlight2R.Rmd'


so it installs the sesameData package (because of 
ExperimentHub::ExperimentHub()[['EH3675']]) , and then fails like that.

We have very little experience in development under Windows and are a bit 
stumped on what might be the problem; do you know whether this error message 
comes from anything in particular or do you have any further idea on how to 
troubleshoot this?

I assume the error message does not refer to connecting to some server on the 
internet, since all works fine on Linux and I can reproduce the problem from 
different machines/connections. But happy to hear your thoughts

Thank you and kind regards,

Matteo Tiberti

Danish 

Re: [Bioc-devel] DataFrame conversion

[Ramos Perez, Marcel via Bioc-devel]

Hi Daniel,

Thanks for posting.

Hervé has asked on the R-devel mailing list:

https://stat.ethz.ch/pipermail/r-devel/2024-March/083265.html

I don't think you will have to do anything in your package.
Once fixed, the messages will go away.

Best regards,

Marcel


On 3/13/24 5:09 PM, Daniel Schulz wrote:

Dear all,

I am maintaining the imcRtools package. Since Monday we have a build error on 
the development version. Most of the errors are attributed to test functions 
which fail now and can be attributed to the below problem.
It seems that currently with R 4.4 and Bioconductor 3.19 the following code 
will throw a warning which it did not in R4.3/Bioconductor 3.18:




x <- S4Vectors::DataFrame(x = c(1,2,4),y=c("A","B","C"))





as.data.frame(x)



  x y

1 1 A

2 2 B

3 4 C

Warning message:

In as.data.frame.numeric(col, optional = optional) :

  Direct call of 'as.data.frame.numeric()' is deprecated.  Use 
'as.data.frame.vector()' or 'as.data.frame()' instead

I don't really understand what changed in R4.4, Bioconductor 3.19 or S4Vectors 
that we get these warnings. However, many functions, specifically test 
functions in our package fail now due to the warning.
Any advice on how to handle this?
Best,
Daniel


--
Daniel Schulz, PhD
Senior Scientist

Bodenmiller Lab
Department of Quantitative Biomedicine & Institute of Molecular Health Sciences
University of Zurich & ETH Z�rich
Winterthurerstrasse 190
8057 Zurich, Switzerland

phone: +41 446356604


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Re: [Bioc-devel] Error installing rtracklayer in BioC devel docker

[Ramos Perez, Marcel via Bioc-devel]

Hi Shraddha,

It looks like Michael has fixed this on GitHub:
https://github.com/lawremi/rtracklayer/commit/86407bbef2d02455053b7b7c96afe9c5ce6949e7

but the fix hasn't been pushed to Bioconductor devel.

In the meantime, you can install the GH version with

BiocManager::install("lawremi/rtracklayer")

Best regards,

Marcel

On 2/15/24 4:09 PM, Shraddha Pai wrote:

Hello BioC community,

Running BiocManager::install(c("rtracklayer”)) returns an error message (see 
below). I’m running this inside a Docker of bioc level version that I just ran 
today. A quick Google search on the handlers.c error turned up no obvious 
solutions.

Anyone else run into this/have a solution? I was able to install 
“GenomicRanges” so it’s not like the package install process isn’t working in 
this setup.

My setup:
docker run \
-e PASSWORD=bioc \
-p 8787:8787 \
-v /Users/spai/software:/home/rstudio/software \
bioconductor/bioconductor_docker:devel

And I’m running Rstudio via localhost:8787 in my browser.
sessionInfo() output below as well.

Thank you,
Shraddha
--


handlers.c: In function ‘R_warnHandler’:
handlers.c:10:11: error: format not a string literal and no format arguments 
[-Werror=format-security]
   10 |   warning(warn_buf);
  |   ^~~~
cc1: some warnings being treated as errors
make: *** [/usr/local/lib/R/etc/Makeconf:191: handlers.o] Error 1
ERROR: compilation failed for package ‘rtracklayer’
* removing ‘/usr/local/lib/R/site-library/rtracklayer’

The downloaded source packages are in
‘/tmp/Rtmp23htnS/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/local/lib/R/library
  packages:
survival
Warning message:
In install.packages(...) :
  installation of package ‘rtracklayer’ had non-zero exit status




sessionInfo()


R Under development (unstable) (2024-02-07 r85873)
Platform: aarch64-unknown-linux-gnu
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  
LAPACK version 3.10.0

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

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

loaded via a namespace (and not attached):
[1] BiocManager_1.30.22 compiler_4.4.0  tools_4.4.0



--
Shraddha Pai, PhD
Principal Investigator
Adaptive Oncology

Assistant Professor
Department of Medical Biophysics
University of Toronto

shraddha@oicr.on.ca

Ontario Institute for Cancer Research
MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
@OICR_news | 
www.oicr.on.ca

Collaborate. Translate. Change lives.

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Elm & Carlton Streets
Buffalo, New York, 14263


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Re: [Bioc-devel] BiocCheck error

[Ramos Perez, Marcel via Bioc-devel]

Hi Marek,

Thanks for pointing this out in release.
I have applied the patch to BiocCheck version 1.38.1.

FWIW, this issue was first opened here
https://github.com/Bioconductor/BiocCheck/issues/135

Best regards,

Marcel

On 1/25/24 9:24 AM, Marek Gierlinski (Staff) wrote:
> Yes, it must be this. I�ve installed the devel version and the error is gone.
>
> Marek
>
> From: Kern, Lori 
> Date: Thursday, 25 January 2024 at 14:13
> To: James W. MacDonald , Marek Gierlinski (Staff) 
> , bioc-devel@r-project.org 
> 
> Subject: Re: BiocCheck error
> I believe this bug with BiocCheck is fixed in the current devel version 
> 1.39.21 but will let the contributor that worked on the bug comment for sure.
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
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>
>
> ___
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-- 
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Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics and Bioinformatics
Elm & Carlton Streets
Buffalo, New York, 14263



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Re: [Bioc-devel] IFAA Bioconductor

[Ramos Perez, Marcel via Bioc-devel]

Hi Zhigang,

AFAICT, I don't see `crossprod` as an exported symbol in `MatrixExtra`.

> library(MatrixExtra)

> ls("package:MatrixExtra")

Did you mean Matrix:: or base:: crossprod?

Best regards,

Marcel


On 1/16/24 10:14 AM, Zhigang Li wrote:

Hi There,

It seems that the error says :
"
** byte-compile and prepare package for lazy loading

Error: object ‘crossprod’ is not exported by 'namespace:MatrixExtra'

"

But we checked and the package "MatrixExtra" still has the function
"crossprod". And in the NAMESPACE file, there is a row for
"importFrom(MatrixExtra,crossprod)". So we are a bit confused why this
error happened. And there was no error for the previous version. Would you
mind providing some advice? Thanks.

Regards,
Zhigang
https://sites.google.com/view/zlab


On Thu, Jan 11, 2024 at 10:11 AM CoreTeam Bioconductor <


bioconductorcoret...@gmail.com> wrote:



Hello Package Maintainer,

We would like to bring to your attention that your package is failing in
devel across all platforms. This is very problematic. Please investigate
the issues and fix the package to avoid deprecation.

https://bioconductor.org/checkResults/devel/bioc-LATEST/


If you have further questions or concerns please reach out on the
bioc-devel@r-project.org

We appreciate your quick attention to this matter

Cheers,
On behalf of the Bioconductor Core Team







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Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263


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Re: [Bioc-devel] Single Package Builder failing to detect subscription to the Bioc-devel mailing list

[Ramos Perez, Marcel via Bioc-devel]

Hi Boyi,

This has been resolved in BiocCheck version 1.39.12.

https://github.com/Bioconductor/BiocCheck/issues/205

Best regards,

Marcel

On 1/10/24 2:53 PM, Boyi Guo wrote:

Hi,

I had the same problem (
https://bioconductor.org/spb_reports/tpSVG_buildreport_20240109095309.html).

* Checking for bioc-devel mailing list subscription...


  * ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel



In my experience, signing up the mailing list again, even though I
already signed up previously, resolved that error.
I am not sure if this practice should be advised, and I did receive an
auto email with subject line "Mailman privacy alert", telling me that
I've already signed up.

Thanks.

Best,

Boyi


On Mon, Jan 8, 2024 at 7:49 AM Kern, Lori via Bioc-devel <
bioc-devel@r-project.org> wrote:



I can confirm that this email is subscribed.  We can open an issue on
BiocCheck to investigate this more.  In the meantime I will comment on your
submission issue to ignore the error for now.



Lori Shepherd - Kern

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 Richard
Heery 
Sent: Sunday, January 7, 2024 7:17 AM
To: bioc-devel@r-project.org 

Subject: [Bioc-devel] Single Package Builder failing to detect
subscription to the Bioc-devel mailing list

Hi all,

My package submission is repeatedly failing due to an error saying I am not
subscribed to the Bioc-devel mailing list, even though I am subscribed
using this email. This is the same email I have in the DESCRIPTION file and
also as my git user.email both globally and locally in the repository. Any
ideas what could be causing this?

Cheers,

Richard

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Buffalo, New York 14263


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Re: [Bioc-devel] S4 accessor conflict (MoleculeExperiement)

[Ramos Perez, Marcel via Bioc-devel]

Hi Nick,

Git blame says the 'molecules' method and generic have been in 
SpatialExperiment for at least 2 years.

It looks like the maintainers of MoleculeExperiment should import the molecules 
generic and export only their method.

The other option is to have a separate package with only SpatialGenerics (à la 
MatrixGenerics) but this would require
considerable collaboration between multiple parties.

Best regards,

Marcel


On 10/29/23 11:02 PM, Nick Robertson via Bioc-devel wrote:

Dear All,


The new update of SpatialExperiement includes a molecules() method, and this 
appears to be causing a conflict with the 
MoleculeExperiement
 molecules() accessor.
When calling  molecules(me, assayName = "detected")​, the following error is 
reported:

unable to find an inherited method for function 'molecules' for signature 
'"MoleculeExperiment"'

Adding MoleculeExperiement:: to the molecules() call fixes the issue, but this 
is not ideal, as it really should not be necessary since a molecules() method 
exists for the MoleculeExperiement class.

Additionally, MoleculeExperiement was explicitly built to be interoperable with 
SpatialExperiement and imports SpatialExperiement::SpatialExperiement() in 
order to output spe objects.

Is there any way to overcome this conflict?

Regards,
Nick

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Buffalo, New York 14263


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Re: [Bioc-devel] KEGGREST is broken and has a long reverse-dependency chain.

[Ramos Perez, Marcel via Bioc-devel]

Thank you for the fix.
I have updated the package.

Best,

Marcel

On 9/21/23 7:12 PM, Ali Sajid Imami wrote:

I'll take a look. I rely on KEGGREST a lot.


Regards,
Dr. Ali Sajid Imami
LinkedIn 



On Thu, Sep 21, 2023 at 7:02 PM Charles Plessy 

wrote:



Dear all,

yesterday I reported on GitHub that the regression tests of KEGGREST
fail because the KEGGREST:::.get.tmp.url function can not parse
www.kegg.jp pages anymore.

https://github.com/Bioconductor/KEGGREST/issues/21

This is a problem in Debian because 1) we do not allow the Bioconductor
packages that we redistribute to fail their tests and 2) the
reverse-dependency chain of KEGGREST is heavy.

KEGGREST <- AnnotationDbi <- GenomicFeatures <- lots of other packages

I am not familiar with KEGG enough to grasp what KEGGREST:::.get.tmp.url
was looking for.  But I was wondering if this bug would be a low-hanging
fruit for somebody else in this list?

Have a nice day,

Charles Plessy

--
Charles Plessy - - ~ ~ ~ ~ ~  ~ ~ ~ ~ ~ - - 
charles.ple...@oist.jp
Okinawa  Institute  of  Science  and  Technology  Graduate  University
Senior staff scientist ~~ Luscombe Unit ~~ https://groups.oist.jp/grsu
Toots from work - ~~  ~~ - https://fediscience.org/@charles_plessy

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---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263


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