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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--
Marcel Ramos Pérez
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics and Bioinformatics
Elm & Carlton Streets
Buffalo, New York, 14263


This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
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recipient(s), you are hereby notified that any disclosure, copying, 
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[Bioc-devel] DataFrame conversion

[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


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

[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>
> |  Facebook<
> 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>
> |  Instagram<
> https://secure-web.cisco.com/1CQuZA_POXzPPQwHz-rwFaOWiACcr2vmbgkZm4SvBxxqCkkPfwv_BVMP33GeJprINJPgY-Vuds0u7-i6fR1Su949v1Nl8X_pwrglILIBbtK0pKoDAPPBUDhm-Dt3QO56boRADBRoUcm9KJToqBL86ArMj7O-SNBYs2UmvyETlFemVr8otTyuhvIiLfIiiiYqKQEPGVYCIQ1U1IUf1ASmjEoZFFxZKKVq-FI6TcC68PD1Fhqc9MvJt0EkTfuFdNwfWuhP_CJHw9kNirzvBAF0K62Og6nMwJNrQGN3zT_61npUKZRl5ob5hxL1suFFn910A/https%3A%2F%2Fwww.instagram.com%2Fwehi_research>
> |  Youtube<
> https://secure-web.cisco.com/1KOXtWRwqSFN7vgGI-h7UZCL75tgW6MqwUYLfiGA6be5eVNV-BX-qKM-c5j6uWX7vDXtGl74Kb94G45WHPaBz0ivuUbcR9e9D2YfxKSOHDZgPs1H4AsdPxi4qkQrH154w6QKKsUiuSmzczLq6iZexpqAd3wNw-l32SeuhnNQUB-nS_I07NC683sJehmM4SX2H4oGN9tkGLrqGBXF5M--qHgIx8ByMfZsirKoA6tIY1giF19ikJjkWYfee6qki4kW-LRryfJzXMR3WY8FoHQbkU9lq2O2J-K2RyzfladjCNtDQdkMJJUkefPdgqSzZk7Cs/https%3A%2F%2Fwww.youtube.com%2Fuser%2FWEHImovies>
> |  LinkedIn<
> 

[Rd] R Dev Day @ Imperial, London, Fri Apr 26

[Heather Turner]

Dear All,

R Dev Day @ Imperial will take place on Friday 26 April at Imperial College 
London:
https://pretix.eu/r-contributors/r-dev-day-imperial-2024/

This event is aimed at current or aspiring R contributors based in the UK. 
Unlike other contributor events, we may not have representation from the R Core 
Team, however it is a chance for interested folk to get together to learn more, 
or to work collaboratively on potential contributions to base R.

This R Dev Day is a satellite to London satRday, Saturday 27 April: 
https://satrday-london-2024.jumpingrivers.com/. Thanks to Jumping Rivers and 
Imperial Central RSE Team, coffee and lunch breaks are catered for participants.

There is no selective application for this event. Registration is free and open 
until Sunday 14 April or until places are filled.

Best wishes,

Heather
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[Bioc-devel] xcms error with R CMD check "checking loading without being on the library search path"

[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

[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

[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: 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. 
Displayed in 
red]>

http://secure-web.cisco.com/10cZJYNnnpHyGbN6ZaJvPeqXtFVn1XO0okme4Cxe0OmSUz_Fn4b54Yxlv_12XxS43PasDRfAw7yK9jKcxc7_w_4bxQOkLYFDot2pJirbjzXKeGyNouv3mg1xHfFYGzIlWDMpMJh7fzBzq0xlzhA7ML5siFCwZ5rwngWp_OTkvte7ZhFlyWgfJlQWNfizw-cQ6VQdEKHMmaWHhG4tpowBAlUfexmkFct5r23-06Wxv03K45E9ImM6tUGPKMsmmlKy4SMclFKuGjEVtITjCd8bJEPs93wGPZCC7kTP6wu4V61zrzAaI_cIfcbC4mJ6cl6uz/http%3A%2F%2Fwww.cancer.dk>
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Re: [Rd] Spurious warning in as.data.frame.factor()

[Ivan Krylov via R-devel]

В Tue, 12 Mar 2024 12:33:17 -0700
Hervé Pagès  пишет:

> The acrobatics that as.data.frame.factor() is going thru in order to 
> recognize a direct call don't play nice if as.data.frame() is an S4 
> generic:
> 
>      df <- as.data.frame(factor(11:12))
> 
>      suppressPackageStartupMessages(library(BiocGenerics))
>      isGeneric("as.data.frame")
>      # [1] TRUE
> 
>      df <- as.data.frame(factor(11:12))
>      # Warning message:
>      # In as.data.frame.factor(factor(11:12)) :
>      #   Direct call of 'as.data.frame.factor()' is deprecated.

How about something like the following:

Index: src/library/base/R/zzz.R
===
--- src/library/base/R/zzz.R(revision 86109)
+++ src/library/base/R/zzz.R(working copy)
@@ -681,7 +681,14 @@
 bdy <- body(as.data.frame.vector)
 bdy <- bdy[c(1:2, seq_along(bdy)[-1L])] # taking [(1,2,2:n)] to insert at 
[2]:
 ## deprecation warning only when not called by method dispatch from 
as.data.frame():
-bdy[[2L]] <- quote(if((sys.nframe() <= 1L || !identical(sys.function(-1L), 
as.data.frame)))
+bdy[[2L]] <- quote(if((sys.nframe() <= 1L || !(
+   identical(sys.function(-1L), as.data.frame) || (
+   .isMethodsDispatchOn() &&
+   methods::is(sys.function(-1L), 'derivedDefaultMethod') &&
+   identical(
+   sys.function(-1L)@generic,
+   structure('as.data.frame', package = 'base')
+   )
.Deprecated(
msg = gettextf(
"Direct call of '%s()' is deprecated.  Use '%s()' or
'%s()' instead",

The patch passes make check-devel, but I'm not sure how to safely put
setGeneric('as.data.frame'); as.data.frame(factor(1:10)) in a
regression test.

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] confusion over spellchecking

[Ivan Krylov via R-package-devel]

В Sun, 10 Mar 2024 13:55:43 -0400
Ben Bolker  пишет:

> I am working on a package and can't seem to get rid of a NOTE about
> 
> Possibly misspelled words in DESCRIPTION:
>glmmTMB (10:88)
>lme (10:82)
> 
> on win-builder.

Do you have these words anywhere else in the package (e.g. in the Rd
files)? It turns out that R has a special environment variable that
makes it ignore custom dictionaries specifically for DESCRIPTION:

>>## Allow providing package defaults but make this controllable via
>>##   _R_ASPELL_USE_DEFAULTS_FOR_PACKAGE_DESCRIPTION_
>>## to safeguard against possible mis-use for CRAN incoming checks.

I cannot see it used anywhere under the trunk/CRAN subdirectory in the
developer.r-project.org Subversion repo, but it could be set somewhere
else on Win-Builder.

-- 
Best regards,
Ivan

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Re: [R-pkg-devel] Submission after archived version

[Ivan Krylov via R-package-devel]

В Mon, 11 Mar 2024 23:45:13 +0100
Nils Mechtel  пишет:

> Despite R CMD check not giving any errors or warnings, the package
> doesn’t pass the pre-tests:

If your question was more about the reasons for the difference between
your R CMD check and the pre-tests, most of it is due to --as-cran:

(Using commit ffe216d from https://github.com/nilsmechtel/MetAlyzer as
the basis for the example, which seems to be different from the
incoming pretest from the link you've shared.)

$ R-devel CMD check MetAlyzer_1.0.0.tar.gz
<...>
Status: OK  
$ R-devel CMD check --as-cran MetAlyzer_1.0.0.tar.gz
<...>
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories: ‘metabolomics_data.csv’
<...>

It's less wasteful to run checks without --as-cran in CI (as you
currently do), but you need to perform additional testing before making
a release. The incoming pre-tests use a custom set of environment
variables that go a but further than just --as-cran:
https://svn.r-project.org/R-dev-web/trunk/CRAN/QA/Kurt/lib/R/Scripts/check_CRAN_incoming.R

In particular, _R_CHECK_CRAN_INCOMING_USE_ASPELL_=true enables the
check for words that are possibly misspelled:

(Using an extra environment variable because your package has been
already published and R filters out "misspellings" found in the CRAN
version of the package. Congratulations!)

$ env \
 _R_CHECK_CRAN_INCOMING_ASPELL_RECHECK_MAYBE_=FALSE \
 _R_CHECK_CRAN_INCOMING_USE_ASPELL_=true \
 R-devel CMD check --as-cran MetAlyzer_1.0.0.tar.gz
<...>
Possibly misspelled words in DESCRIPTION:
  metabolomics (15:78)
<...>

Yet another way to avoid false misspellings is to create a custom
dictionary:
http://dirk.eddelbuettel.com/blog/2017/08/10/#008_aspell_cran_incoming

$ mkdir -p .aspell
$ echo '
 Rd_files <- vignettes <- R_files <- description <- list(
  encoding = "UTF-8",
  language = "en",
  dictionaries = c("en_stats", "dictionary")
 )
' > .aspell/defaults.R
$ R -q -s -e '
 saveRDS(c(
  "metabolomics" # , extra words go here
 ), file.path(".aspell", "dictionary.rds"))
'
$ R CMD build .
$ env \
 _R_CHECK_CRAN_INCOMING_ASPELL_RECHECK_MAYBE_=FALSE \
 _R_CHECK_CRAN_INCOMING_USE_ASPELL_=true \
 R-devel CMD check --as-cran MetAlyzer_1.0.0.tar.gz
# No more "Possibly misspelled words in DESCRIPTION"!

Some day, this will be documented in Writing R Extensions, or maybe in
R Internals (where the other _R_CHECK_* variables are documented), or
perhaps in the CRAN policy. See also:
https://stat.ethz.ch/pipermail/r-package-devel/2024q1/010558.html

-- 
Best regards,
Ivan

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