Re: [Bioc-devel] BiocFileCache Caching ERROR on devel builders
This might be the structToolbox package. I have reverted the part of the commit where I made changes to the cache location and pushed to devel (I didnt make changes to cache location on release branch). Hopefully that is enough to correct it. Apologies to everyone for any issues I may have inadvertently caused. Best regards, Gavin From: Bioc-devel on behalf of lori.sheph...@roswellpark.org Sent: 30 July 2021 19:23 To: bioc-devel@r-project.org Subject: [Bioc-devel] BiocFileCache Caching ERROR on devel builders We are seeing a BiocFileCache default directory ERROR appearing on the devel build reports. This seems to be a recent ERROR, introduced sometime in the last week, and we are trying to track down the offending package that builds the location. If you see this ERROR in your package you may ignore for now -- If you are the culprit of building this location, please fix asap. 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 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 sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] ExperimentHub package development - Windows OS specific error
I did not get this error on my Windows machine; ExperimentHub can find the
alzzh_gwas_top100 dataset in Bioc 3.13 (devel).
Your snapshot date is older than mine. R reported my snapshot date as
"2021-03-02"
Maybe you need to clear the cache?
You can request all available snapshot dates with possibleDates and set a
specific one if you want to with snapshotDate. See ?ExperimentHub for info.
I am not sure what best practice would be in terms of Bioc 3.13 (should you fix
a snapshot date in your package, or always use the most recent date, or allow
the user to specify a snapshot date...?). You could ask your reviewer for
advice in this regard, or maybe someone on the mailing list will comment.
Gavin
From: Murphy, Alan E
Sent: 02 March 2021 20:07
To: Gavin Lloyd (College of Medical and Dental Sciences);
bioc-devel@r-project.org
Subject: Re: ExperimentHub package development - Windows OS specific error
Hey Gavin,
This worked perfectly, thanks!
However, this did lead to another error where one of the datasets from the
metadata file wasn't found in the ExperimentHub dataset. Again this is Windows
specific and the dataset in question (alzh_gwas_top100) does exist:
> ### ** Examples
>
> alzh_gwas_top100()
using temporary cache D:\temp\RtmpCEujsj/working_dir\RtmpY9HMAa/BiocFileCache
snapshotDate(): 2020-04-27
Error in alzh_gwas_top100() :
resource alzh_gwas_top100 not found in ExperimentHub
This error is thrown in zzz.R here:
objs <- read.csv(system.file("extdata", "metadata.csv",
package="ewceData"),
stringsAsFactors=FALSE,fileEncoding = "UTF-8-BOM")$Title
if (!length(objs))
stop("no objects found")
## Functions to load objects by name:
ns <- asNamespace(pkgname)
sapply(objs,
function(xx) {
func = function(metadata = FALSE) {
if (!isNamespaceLoaded("ExperimentHub"))
attachNamespace("ExperimentHub")
eh <- query(ExperimentHub(), "ewceData")
ehid <- names(query(eh, xx))
if (!length(ehid))
stop(paste0("resource ", xx,
" not found in ExperimentHub"))
if (metadata)
eh[ehid]
else eh[[ehid]]
}
assign(xx, func, envir=ns)
namespaceExport(ns, xx)
})
I checked and objs does contain the correct list of titles so the issue isn't
there. Sorry about the continuation in the question but does anyone know why
this could be happening?
Kind regards,
Alan.
From: Gavin Lloyd
Sent: 02 March 2021 18:10
To: Murphy, Alan E ; bioc-devel@r-project.org
Subject: Re: ExperimentHub package development - Windows OS specific error
This email from g.r.ll...@bham.ac.uk originates from outside Imperial. Do not
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Your file seems to be encoded as UTF-8-BOM.
When I read it in on my Windows 10 machine the Title column has extra
characters at the front ("�..Title"), which is why your function returns "no
object found" when checking for the Title column.
If I resave your file with UTF-8 format your function works as expected and I
am able to install your package.
Gavin
From: Bioc-devel on behalf of Murphy, Alan E
Sent: 02 March 2021 17:00
To: bioc-devel@r-project.org
Subject: [Bioc-devel] ExperimentHub package development - Windows OS specific
error
Hi all,
My apologies, I have emailed before on a related issue but now think I have
found a potential cause of the issue I am having but can't seem to find a fix.
I am working on an ExperimentHub data package;
ewceData<https://github.com/neurogenomics/ewceData>, which fails checks on
Windows OS but passes on Linux and Mac. On Windows, the package fails to
install with the following output:
Error: package or namespace load failed for 'ewceData':
.onLoad failed in loadNamespace() for 'ewceData', details:
call: fun(libname, pkgname)
error: no objects found
Error: loading failed
Execution halted
It seems like this error is caused by my onload function. The onload function I
use (zzz.R) should allow easy access to the stored datasets, allowing a user to
call the dataset like dataset1(). The error note printed appears because the
metadata.csv file did not read properly
.onLoad <- function(libname, pkgname) {
objs <- read.csv(system.file("extdata", "metadata.csv",
package="ewceData"),
stringsAsFactors=FALSE)$Ti
Re: [Bioc-devel] ExperimentHub package development - Windows OS specific error
Your file seems to be encoded as UTF-8-BOM.
When I read it in on my Windows 10 machine the Title column has extra
characters at the front ("�..Title"), which is why your function returns "no
object found" when checking for the Title column.
If I resave your file with UTF-8 format your function works as expected and I
am able to install your package.
Gavin
From: Bioc-devel on behalf of Murphy, Alan E
Sent: 02 March 2021 17:00
To: bioc-devel@r-project.org
Subject: [Bioc-devel] ExperimentHub package development - Windows OS specific
error
Hi all,
My apologies, I have emailed before on a related issue but now think I have
found a potential cause of the issue I am having but can't seem to find a fix.
I am working on an ExperimentHub data package;
ewceData, which fails checks on
Windows OS but passes on Linux and Mac. On Windows, the package fails to
install with the following output:
Error: package or namespace load failed for 'ewceData':
.onLoad failed in loadNamespace() for 'ewceData', details:
call: fun(libname, pkgname)
error: no objects found
Error: loading failed
Execution halted
It seems like this error is caused by my onload function. The onload function I
use (zzz.R) should allow easy access to the stored datasets, allowing a user to
call the dataset like dataset1(). The error note printed appears because the
metadata.csv file did not read properly
.onLoad <- function(libname, pkgname) {
objs <- read.csv(system.file("extdata", "metadata.csv",
package="ewceData"),
stringsAsFactors=FALSE)$Title
if (!length(objs))
stop("no objects found")
It would seem the issue is with either read.csv or system.file and is specific
to Windows OS. Just to note I also do import read.csv from utils.
If anyone has come across an issue like this before or have good guesses for a
possible fix it would be greatly appreciated?
Kind regards,
Alan,
Alan Murphy
Bioinformatician
Neurogenomics lab
UK Dementia Research Institute
Imperial College London
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Re: [Bioc-devel] Cannot reproduce a regionReport 1.21.7 error on the Bioc 3.11 Linux builder
I also had an issue related to cropping using BiocStyle pdf_document, and used the same fix. https://github.com/Bioconductor/BiocStyle/issues/75 Gavin From: Bioc-devel on behalf of mtmorgan.b...@gmail.com Sent: 24 April 2020 11:26:30 To: Leonardo Collado Torres; Bioc-devel Cc: Andrzej Oleś Subject: Re: [Bioc-devel] Cannot reproduce a regionReport 1.21.7 error on the Bioc 3.11 Linux builder Thanks for the detective work Leo; to me it sounds like, for robust output (function more important than form) BiocStyle should not try to crop images. Martin On 4/24/20, 12:52 AM, "Bioc-devel on behalf of Leonardo Collado Torres" wrote: Hi Bioc-devel again, I believe that I have found the source of my regionReport problem and a workaround. We'll know tomorrow if it goes through the Bioc builds but it works at https://github.com/leekgroup/regionReport/actions/runs/86364716. The problem is related to https://github.com/ropensci/magick/issues/171 and similar issues. The workaround is to use `crop = NULL` on R Markdown code chunks to disable the default image cropping behavior by BiocStyle::html_document, and thus avoid cache issues from magick (R) and ImageMagick (not R). Both the Bioc-devel Linux machine and GitHub Actions using Bioconductor devel run into a problem where there's not enough resources in the cache for cropping the images produced by regionReport::derfinderReport(). Either (a) the Bioc-devel Windows and macOS machines don't have magick installed (so no cropping gets attempted), (b) use a compiled version of magick that ships with the right version of ImageMagick, or (c) they have more resources than the bioc Linux build machine and the bioc devel docker running on GHA Linux In any case, disabling cropping circumvents this issue. Here's the full investigative report. ## A new lead I recently stumbled upon [1] and re-reading it now I see that they link to [2] which mentions that BiocStyle crops by default and that this can be turned off using `crop = NULL`. regionReport uses BiocStyle::html_document both for its vignettes as well as the reports it makes by default. Actually at [3], which was built using the Bioconductor devel docker & GitHub Actions (GHA), I see tons of messages that are similar to: ## The magick package is required to crop "basicExploration_files/figure-html/pvals-1.png" but not available. For reference, [4] is how that example from regionReport::derfinderReport() looks built using GHA. I copied the log of messages to a gist at [5]. From [6] I found [7] where Mike Smith explains to Aaron Lun the default behavior of BiocStyle and again suggests to use `crop = NULL` just like Yihui Xie mentioned earlier at [2]. I see at [8] that Kevin Rue-Albrecht also ran into a `crop = NULL` problem in iSEE. So I have a good lead now! ## Adding magick to Suggests We can see clearly that magick is not available on my GitHub Actions run using the Biocondutor devel docker: regionReport 1.21.7 doesn't mention magick on it's DESCRIPTION so it's never installed on GHA. However, magick is likely installed on the Bioconductor 3.11 Linux build machine and thus it is used for cropping. At [9] I bumped regionReport to 1.21.8 after adding magick to suggests. Actually, this is what Yihui Xie recommends BiocStyle could/should do in [2]. That crashed and burned on GHA Linux with Bioc-docker at [10], thus reproducing the Linux build machine error. Quitting from lines 224-229 (basicExploration.Rmd) 35Error: processing vignette 'regionReport.Rmd' failed with diagnostics: 36R: cache resources exhausted `/tmp/RtmpfaoqUE/Rbuild74c3a6bf655/regionReport/vignettes/report/html/basicExploration_files/figure-html/plotRegions-17.png' @ error/cache.c/OpenPixelCache/4083 Actually, this error message is more informative than the one from the Bioc Linux builder as it gives the actual image name where it all burned down. ## Moving problematic code from the vignette to an example At [11] I moved the problematic code to an example instead of the vignette. On GHA, it failed again at [12] predictably on another image than in [10]. Also predictably, R CMD build worked this time, but R CMD check failed. However, now the I get the full logs that help me see the details much better and link it to code [13] (so if that was the bug source, I would know where to look). Quitting from lines 399-400 (basicExploration.Rmd) 355Error in magick_image_trim(image, fuzz) : 356 R: cache resources exhausted `/__w/regionReport/regionReport/check/regionReport.Rcheck/derfinderReport-example/basicExploration/basicExploration_files/figure-html/genomeOverview3-1.png' @ error/cache.c/OpenPixelCache/4083 357Calls:
