Re: [Bioc-devel] DataFrame conversion

2024-03-13 Thread 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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Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics and Bioinformatics
Elm & Carlton Streets
Buffalo, New York, 14263


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[Bioc-devel] DataFrame conversion

2024-03-13 Thread Daniel Schulz 
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


[[alternative HTML version deleted]]

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Re: [Bioc-devel] Failed to activate account for Bioconductor git credentials

2024-03-13 Thread Małgorzata Oleś 
Dear Lori,

the issue described by Ning seems to be the same as I am experiencing right
now (new machine + public key in github updated + Bioconductor Git
Credentials not recognising my email + g...@git.bioconductor.org: Permission
denied (publickey)). Could you assist me here, please?

Best wishes,
Małgorzata

On Fri, Jan 26, 2024 at 8:07 PM Kern, Lori via Bioc-devel <
bioc-devel@r-project.org> wrote:

> We have located the source of the ERROR with push access. As this involves
> some other information I will email you off list for resolution.
>
> Cheers,
>
>
> 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 Ning Liu
> via Bioc-devel 
> Sent: Wednesday, January 24, 2024 12:26 AM
> To: bioc-devel@r-project.org 
> Subject: [Bioc-devel] Failed to activate account for Bioconductor git
> credentials
>
> Hi,
>
> I�m the maintainer for standR and hoodscanR packages.
>
> I recently changed my work laptop and now found that I don�t have the
> access to upstream, i.e. g...@git.bioconductor.org:
> packages/standR.git
> and g...@git.bioconductor.org:packages/hoodscanR.git g...@git.bioconductor.org:packages/hoodscanR.git> anymore, getting this
> error:
> g...@git.bioconductor.org: Permission denied (publickey).
> fatal: Could not read from remote repository.
>
> I�ve updated the ssh key in my github account to with my new laptop�s
> public key. But I�m having trouble to login to
> https://secure-web.cisco.com/1NZmR5W0tUTOb0CObyvMSfwnnKp7F0DmAvhQhjyniL7GE46EdoAmPGZJyIfPAlMCVydbs-TpgLnfjjHVD08nSeCMvjN2nL0DrL8qP3nGVfHQgwCOWF6pcFO2MW4XA2QOjSB9Utvi-6MhAxyGa09w4YJpwGr6opGSofgqUSAWu7p0q7-h2hFtb949-Vm34ZYTyR8-alzMmjycQkZICejTKmgvhOJuPCWbJLXNwQpCKYBttbOBoDOQl-NwTAC5YFbn7k6A7Tt64SvxuBljo96C7J0rfcSkTHYsfZmvis70PuBab7-_vqQiPhQrGfu2YiKoK/https%3A%2F%2Fgit.bioconductor.org%2FBiocCredentials%2Flogin%2F%3Fnext%3D%2FBiocCredentials%2F
> to manage my credentials, when I tried to activate my account it said �
> li...@wehi.edu.au is not associated with a maintainer of a Bioconductor
> package.�
>
> Can you help me with this?
>
> Cheers,
> Ning
>
> [WEHI Logo]
>
>
> Walter and Eliza Hall Institute of Medical Research
> 1G Royal Parade Parkville Victoria 3052 Australia
>
>
> http://secure-web.cisco.com/1le100tie6MZO20dzn_w4VLP2YHoo5eKINIgZCCv5p4VDS5pGx5UaC4YsAs8VW5nT8tTVVVWt6359YmFaPsZGZwLyyTBlxgJbi6cPG64iDwPldHkHSNRn1FPt4ID62stEplBAsCmkVa41bclUoNbpnh2tajWfzVJpQFBrSOebvofyhT0AXZDBxSAoZWwZ4S81oMU8B5I0MXfHIDKYwIHrWAE5A4Nc__twPYTuI0RzYm0G6eZYsWURHD7A7fBL1gQzWS0tVbq8Tjv_l5mi7Cqkfm-dvYQtguc29R4hrJpa5zO_eA1lZhFYrPeukYxQrN3t/http%3A%2F%2Fwww.wehi.edu.au
> <
> https://secure-web.cisco.com/1cwI1EnrpsU7GS6IPGf5BPuwxFJHtS8evt9fjWXZydFTelAtAxdk3U0MiaQyqX1mCBgIVL_L3aq9617Foz0svP5RmmXz-tY3kIeauzl-IZRV18TFGTv2IEm7DSTrnlEus-UTv47uL3fyhKSmLRAwtdKN8erKWU0uTePUCq415RjXq5F3-KMn1z6ZZLaP0WbnbHLG-507_x3cmrimEFeq2eQ0HPkcm6NlWV20cSzvxISbxVgroY38_YZq9NNuXwGVP4qwI00XpVX2LJ8AWD97_iHDc2v3LnMCeNBOrhkyardN55c78skLuXvU2wfnBybwd/https%3A%2F%2Fwehi.edu.au
> >
>
> Twitter<
> https://secure-web.cisco.com/1SdpK3rSB-eTgQwXPG_NdEusB1GXoWojgJJj5BNf8TFtoKN9G98pInWHdVo9WI1F-7g7pVkj7wGt5ceKsaNRLYdNBGSoLYq8UJbr-O-kCqPzGzA8nTiFMWueF5RxExNTpdb5o2dj1PbE3VqWUbL2GucWzDHheupnsDfeye2joL-4jHYEXGcawvjdFluyPfBc9KI-udtmxE1E-9hhjmQI8AVjESm-zUx0gGKet0RgrWXhkKKwUAtiC8Nnds1Z54U-CDCNtqSY__Eg1GXxDQ4f6_KodRmzAWiw4H_ttPT27oZpGqMJ8JS6Notihj6RD0i_X/https%3A%2F%2Ftwitter.com%2FWEHI_research>
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> https://secure-web.cisco.com/1SwJIeuJsPnQZRCNTrlqi8Dy3BAfMOl2F7d4PcSJhHo-aH74MKVts-Aa_0dH6nVqLyxSlwZgr2tCvgvxdhT6Z53JOQ_Z36FHO1g-oUwuhmiXjuPfLWh0YLlqIkBzvOoBx07n1cIZhPNeo_158AkSK1hG5-BKk7DrtK6Xq4Pv-maP85_TwGzjXzWMkEZQzgh0WNrbEOnBq_Lptk5Mn_BrGdzQguYTLgMxAQwVamGeHZf-u3yanGnjDWf_ZE0Qu-Ji5n_Ag144iR-Tz8Nk109ytjcfx-Cx2jBDrYFilT9zAKkWOmVb9xOdB2AupCz9XKJls/https%3A%2F%2Fwww.facebook.com%2FWEHIresearch%2F>
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[Bioc-devel] xcms error with R CMD check "checking loading without being on the library search path"

2024-03-13 Thread Rainer Johannes 
Dear all,

we're having some rather strange errors with R CMD check on the xcms package 
recently: it will fail with this warning (which then becomes an error):

✔  checking whether the namespace can be loaded with stated dependencies (5.9s)
✔  checking whether the namespace can be unloaded cleanly (6.1s)
W  checking loading without being on the library search path (5.3s)
   Loading required package: BiocParallel
   Loading required package: MSnbase
   Loading required package: BiocGenerics

   Attaching package: ‘BiocGenerics’

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

   IQR, mad, sd, var, xtabs

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

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

   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: mzR
   Loading required package: Rcpp
   Loading required package: S4Vectors
   Loading required package: stats4

   Attaching package: ‘S4Vectors’

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

   findMatches

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

   I, expand.grid, unname

   Loading required package: ProtGenerics

   Attaching package: ‘ProtGenerics’

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

   smooth


   This is MSnbase version 2.28.1
 Visit https://lgatto.github.io/MSnbase/ to get started.


   Attaching package: ‘MSnbase’

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

   trimws

   Loading required package: RCurl
   Error: package or namespace load failed for ‘xcms’ in 
.requirePackage(package):
unable to find required package ‘RCurl’
   In addition: Warning message:
   In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return 
= TRUE,  :
 there is no package called ‘RCurl’
   Execution halted

   It looks like this package has a loading problem when not on .libPaths:
   see the messages for details.


This is rather puzzling, since we're not using, requiring or importing RCurl at 
all. Also, so far I've never seen this check "checking loading without being on 
the library search path" before.

I will try to figure out what is going on and where/which package is causing 
this problem, but would be great if someone has a solution or at least a hint.

thanks!
jo

I was running this for xcms from the RELEASE_3_18 branch using the 
bioconductor/bioconductor_docker:RELEASE_3_18. The sessionInfo (after loading 
xcms):

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-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
 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

attached base packages:
[1] stats4stats graphics  grDevices utils datasets  methods
[8] base

other attached packages:
[1] xcms_4.0.2  MSnbase_2.28.1  ProtGenerics_1.34.0
[4] S4Vectors_0.40.2mzR_2.36.0  Rcpp_1.0.11
[7] Biobase_2.62.0  BiocGenerics_0.48.1 BiocParallel_1.36.0

loaded via a namespace (and not attached):
 [1] bitops_1.0-7rlang_1.1.1
 [3] magrittr_2.0.3  clue_0.3-65
 [5] MassSpecWavelet_1.68.0  matrixStats_1.2.0
 [7] compiler_4.3.2  callr_3.7.3
 [9] vctrs_0.6.4 pkgconfig_2.0.3
[11] MetaboCoreUtils_1.11.1  crayon_1.5.2
[13] XVector_0.42.0  utf8_1.2.4
[15] ps_1.7.5preprocessCore_1.64.0
[17] MultiAssayExperiment_1.28.0 zlibbioc_1.48.0
[19] GenomeInfoDb_1.38.7 progress_1.2.3
[21] DelayedArray_0.28.0 parallel_4.3.2
[23] prettyunits_1.2.0   cluster_2.1.4
[25] R6_2.5.1RColorBrewer_1.1-3
[27] limma_3.58.1GenomicRanges_1.54.1
[29] SummarizedExperiment_1.32.0 iterators_1.0.14
[31] IRanges_2.36.0  igraph_2.0.2
[33] Matrix_1.6-5splines_4.3.2
[35] tidyselect_1.2.1abind_1.4-5
[37] doParallel_1.0.17   codetools_0.2-19
[39] affy_1.80.0

Re: [Bioc-devel] AnnotationHub corrupted cache on nebbiolo1

2024-03-13 Thread Matteo Tiberti via Bioc-devel 

Hi,

I can confirm it did clean up – thanks for your help!

Cheers

Matteo Tiberti

Danish Cancer Institute
Strandboulevarden 49
DK-2100 Copenhagen
Telephone: +45 35 25 73 07
– a part of the Danish Cancer Society

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in 
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policy

From: Kern, Lori 
Date: Monday, 11 March 2024 at 17.16
To: bioc-devel@r-project.org , Matteo Tiberti 

Subject: Re: AnnotationHub corrupted cache on nebbiolo1
I noticed that as well and just did the necessary steps to clean the cache. I 
expect this to clean up on the next build.




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 Matteo Tiberti via 
Bioc-devel 
Sent: Monday, March 11, 2024 12:11 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] AnnotationHub corrupted cache on nebbiolo1

Dear BioC developers,

We are getting a strange test fail for our Moonlight2R package when tests are 
run on nebbiolo1 (Linux) only:

ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
 Error: Corrupt Cache: index file
   See AnnotationHub's TroubleshootingTheHubs vignette section on corrupt cache
   cache: /home/biocbuild/.cache/R/AnnotationHub
   filename: annotationhub.index.rds
 Backtrace:
 ▆
  1. └─Moonlight2R::DMA(...) at test-DMA.R:14:1
  2.   └─Moonlight2R::LiftMAF(Infile = mut_only, Current_Build = "GRCh38")
  3. └─AnnotationHub::AnnotationHub()
  4.   └─AnnotationHub::.Hub(...)
  5. └─AnnotationHub:::.db_create_index(hub)

This doesn’t happen to us when testing locally, so we were wondering if there’s 
any problem on the builder or is it anything we can fix ourselves?

Many thanks

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. 
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