Re: [Rd] Marking a ticket as a (potential) regression in bug tracker?
On Fri, Jun 12, 2020 at 10:17:11AM -0400, Scott Kostyshak wrote: > > Is there a way to mark a ticket as a potential regression in the bug > tracker? I think the following issue is a regression: > > https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17684 > > I've just tested (2020-06-12 r78687) and what I believe to be a > regression is still there. I don't think the bug has bitten many people, > so I don't think it is critical, but often it is helpful to mark bugs as > regressions in trackers. If there's no current way to mark something as a regression, would there be support for adding a way? Best, Scott -- Scott Kostyshak (he/him) Assistant Professor of Economics University of Florida https://people.clas.ufl.edu/skostyshak/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [R-pkg-devel] devtools::release() does not release
Maybe off-topic, but I see that the tarball is 100+Mb ... won't that
raise flags upon CRAN submission? (The current CRAN tarball is <1 Mb ...)
From the CRAN policies, there's no explicit limit given but ...
=
Packages should be of the minimum necessary size. Reasonable compression
should be used for data (not just .rda files) and PDF documentation:
CRAN will if necessary pass the latter through qpdf.
As a general rule, neither data nor documentation should exceed 5MB
(which covers several books). A CRAN package is not an appropriate way
to distribute course notes, and authors will be asked to trim their
documentation to a maximum of 5MB.
Where a large amount of data is required (even after compression),
consideration should be given to a separate data-only package which can
be updated only rarely (since older versions of packages are archived in
perpetuity).
Similar considerations apply to other forms of “data”, e.g., .jar files.
On 11/26/20 5:52 PM, Duncan Murdoch wrote:
Why not use the CRAN submission web page, as documented here:
https://cran.r-project.org/web/packages/policies.html#Submission?
Duncan Murdoch
On 26/11/2020 2:57 p.m., Gábor Csárdi wrote:
Why not submit a bug report at the devtools repository?
❯ packageDescription("devtools")$BugReports
[1] "https://github.com/r-lib/devtools/issues;
Gabor
On Thu, Nov 26, 2020 at 7:50 PM Spencer Graves
wrote:
Hi folks,
devtools::release() gave the following errors:
...
Ready to submit fda (5.1.7) to CRAN?
1: Not yet
2: Absolutely
3: U... Maybe?
Selection: 2
Uploading package & comments
Confirming submission
Error in if (new_url$query$submit == "1") { : argument is of length zero
In addition: Warning messages:
1: In charToRaw(enc2utf8(val)) :
argument should be a character vector of length 1
all but the first element will be ignored
2: In charToRaw(enc2utf8(val)) :
argument should be a character vector of length 1
all but the first element will be ignored
Jim Ramsay got this after setwd to what seemed to be the
appropriate
working directory and then running devtools::release(), as noted above.
As near as both of us can determine, we've followed essentially the same
protocol here as with other package submissions.
In case you want the entire devtools::release()
transcript, it
appears below running under Big Sur on a Mac.
Suggestions?
Thanks,
Spencer Graves & Jim Ramsay
——
devtools::release()
Have you checked for spelling errors (with `spell_check()`)?
1: Not yet
2: Nope
3: Absolutely
Selection: 3
Have you run `R CMD check` locally?
1: Yes
2: I forget
3: No
Selection: 1
── Running additional devtools checks for fda
Checking version number has three components... OK
Checking dependencies don't rely on dev versions... OK
Checking DESCRIPTION doesn't have Remotes field... OK
──
Were devtool's checks successful?
1: I forget
2: No
3: Absolutely
Selection: 3
Have you fixed all existing problems at
https://cran.rstudio.com//web/checks/check_results_fda.html ?
1: Yes
2: Not yet
3: No
Selection: 1
Have you checked on R-hub (with `check_rhub()`)?
1: Not yet
2: I forget
3: Definitely
Selection: 3
Have you checked on win-builder (with `check_win_devel()`)?
1: No
2: Nope
3: Absolutely
Selection: 3
Have you checked the 67 reverse dependencies (with the revdepcheck
package)?
1: Definitely
2: No
3: U... Maybe?
Selection: 1
Have you updated `NEWS.md` file?
1: U... Maybe?
2: No
3: Yeah
Selection: 3
Have you updated `DESCRIPTION`?
1: Yup
2: Nope
3: I forget
Selection: 1
Have you updated `cran-comments.md?`
1: Nope
2: Not yet
3: Yeah
Selection: 3
── Running Git checks for fda
Current branch: master
Checking uncommitted files...
WARNING: All files should be tracked and committed before release.
Please add and commit.
Checking synchronisation with remote branch...
ERROR: Error in 'git2r_remote_fetch': unsupported URL protocol
──
Were Git checks successful?
1: Not yet
2: Nope
3: Yup
Selection: 3
Is your email address ram...@psych.mcgill.ca?
1: Yup
2: I forget
3: U... Maybe?
Selection: 1
Building
✓ checking for file
‘/Users/jamesramsay/Documents/R/fda_work/fda/DESCRIPTION’ (437ms)
─ preparing ‘fda’: (5.8s)
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell
scripts (1.6s)
─ checking for empty or unneeded directories
─ building ‘fda_5.1.7.tar.gz’
Submitting file:
/var/folders/sc/6zzfzqbs5w7dl8q5g18tlqfcgn/T//RtmpbcSyMD/fda_5.1.7.tar.gz
File size: 102.9 Mb
Ready to submit fda (5.1.7) to CRAN?
1: Not yet
2: Absolutely
3: U... Maybe?
Selection: 2
Uploading package & comments
Confirming submission
Error in if
Re: [R-pkg-devel] devtools::release() does not release
Why not use the CRAN submission web page, as documented here:
https://cran.r-project.org/web/packages/policies.html#Submission?
Duncan Murdoch
On 26/11/2020 2:57 p.m., Gábor Csárdi wrote:
Why not submit a bug report at the devtools repository?
❯ packageDescription("devtools")$BugReports
[1] "https://github.com/r-lib/devtools/issues;
Gabor
On Thu, Nov 26, 2020 at 7:50 PM Spencer Graves
wrote:
Hi folks,
devtools::release() gave the following errors:
...
Ready to submit fda (5.1.7) to CRAN?
1: Not yet
2: Absolutely
3: U... Maybe?
Selection: 2
Uploading package & comments
Confirming submission
Error in if (new_url$query$submit == "1") { : argument is of length zero
In addition: Warning messages:
1: In charToRaw(enc2utf8(val)) :
argument should be a character vector of length 1
all but the first element will be ignored
2: In charToRaw(enc2utf8(val)) :
argument should be a character vector of length 1
all but the first element will be ignored
Jim Ramsay got this after setwd to what seemed to be the appropriate
working directory and then running devtools::release(), as noted above.
As near as both of us can determine, we've followed essentially the same
protocol here as with other package submissions.
In case you want the entire devtools::release() transcript, it
appears below running under Big Sur on a Mac.
Suggestions?
Thanks,
Spencer Graves & Jim Ramsay
——
devtools::release()
Have you checked for spelling errors (with `spell_check()`)?
1: Not yet
2: Nope
3: Absolutely
Selection: 3
Have you run `R CMD check` locally?
1: Yes
2: I forget
3: No
Selection: 1
── Running additional devtools checks for fda
Checking version number has three components... OK
Checking dependencies don't rely on dev versions... OK
Checking DESCRIPTION doesn't have Remotes field... OK
──
Were devtool's checks successful?
1: I forget
2: No
3: Absolutely
Selection: 3
Have you fixed all existing problems at
https://cran.rstudio.com//web/checks/check_results_fda.html ?
1: Yes
2: Not yet
3: No
Selection: 1
Have you checked on R-hub (with `check_rhub()`)?
1: Not yet
2: I forget
3: Definitely
Selection: 3
Have you checked on win-builder (with `check_win_devel()`)?
1: No
2: Nope
3: Absolutely
Selection: 3
Have you checked the 67 reverse dependencies (with the revdepcheck
package)?
1: Definitely
2: No
3: U... Maybe?
Selection: 1
Have you updated `NEWS.md` file?
1: U... Maybe?
2: No
3: Yeah
Selection: 3
Have you updated `DESCRIPTION`?
1: Yup
2: Nope
3: I forget
Selection: 1
Have you updated `cran-comments.md?`
1: Nope
2: Not yet
3: Yeah
Selection: 3
── Running Git checks for fda
Current branch: master
Checking uncommitted files...
WARNING: All files should be tracked and committed before release.
Please add and commit.
Checking synchronisation with remote branch...
ERROR: Error in 'git2r_remote_fetch': unsupported URL protocol
──
Were Git checks successful?
1: Not yet
2: Nope
3: Yup
Selection: 3
Is your email address ram...@psych.mcgill.ca?
1: Yup
2: I forget
3: U... Maybe?
Selection: 1
Building
✓ checking for file
‘/Users/jamesramsay/Documents/R/fda_work/fda/DESCRIPTION’ (437ms)
─ preparing ‘fda’: (5.8s)
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell
scripts (1.6s)
─ checking for empty or unneeded directories
─ building ‘fda_5.1.7.tar.gz’
Submitting file:
/var/folders/sc/6zzfzqbs5w7dl8q5g18tlqfcgn/T//RtmpbcSyMD/fda_5.1.7.tar.gz
File size: 102.9 Mb
Ready to submit fda (5.1.7) to CRAN?
1: Not yet
2: Absolutely
3: U... Maybe?
Selection: 2
Uploading package & comments
Confirming submission
Error in if (new_url$query$submit == "1") { : argument is of length zero
In addition: Warning messages:
1: In charToRaw(enc2utf8(val)) :
argument should be a character vector of length 1
all but the first element will be ignored
2: In charToRaw(enc2utf8(val)) :
argument should be a character vector of length 1
all but the first element will be ignored
__
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Re: [Bioc-devel] Query on updating version for bioconda-bambu
bioconda is not maintained by Bioconductor, you should ask through bioconda support channels https://bioconda.github.io/ maybe as an issue on their github repository? Martin On 11/25/20, 8:36 PM, "Bioc-devel on behalf of CHEN Ying" wrote: Hello BioC community, I have recently updated the version of bambu with some small bug fixes. I noted that however, the available bionconda-bambu version is still 1.0.0. Could you advise on how to update bionconda-bambu to the most recent version? Thank you Regards, CHEN Ying This e-mail and any attachments are only for the use of the intended recipient and may contain material that is confidential, privileged and/or protected by the Official Secrets Act. If you are not the intended recipient, please delete it or notify the sender immediately. Please do not copy or use it for any purpose or disclose the contents to any other person. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [R-pkg-devel] devtools::release() does not release
Why not submit a bug report at the devtools repository?
❯ packageDescription("devtools")$BugReports
[1] "https://github.com/r-lib/devtools/issues;
Gabor
On Thu, Nov 26, 2020 at 7:50 PM Spencer Graves
wrote:
>
> Hi folks,
>
>
> devtools::release() gave the following errors:
>
>
> ...
> Ready to submit fda (5.1.7) to CRAN?
> 1: Not yet
> 2: Absolutely
> 3: U... Maybe?
>
> Selection: 2
> Uploading package & comments
> Confirming submission
> Error in if (new_url$query$submit == "1") { : argument is of length zero
> In addition: Warning messages:
> 1: In charToRaw(enc2utf8(val)) :
> argument should be a character vector of length 1
> all but the first element will be ignored
> 2: In charToRaw(enc2utf8(val)) :
> argument should be a character vector of length 1
> all but the first element will be ignored
>
>
> Jim Ramsay got this after setwd to what seemed to be the appropriate
> working directory and then running devtools::release(), as noted above.
> As near as both of us can determine, we've followed essentially the same
> protocol here as with other package submissions.
>
>
> In case you want the entire devtools::release() transcript, it
> appears below running under Big Sur on a Mac.
>
>
> Suggestions?
> Thanks,
> Spencer Graves & Jim Ramsay
>
>
> > ——
> >
> > devtools::release()
> >
> > Have you checked for spelling errors (with `spell_check()`)?
> > 1: Not yet
> > 2: Nope
> > 3: Absolutely
> >
> > Selection: 3
> > Have you run `R CMD check` locally?
> > 1: Yes
> > 2: I forget
> > 3: No
> >
> > Selection: 1
> > ── Running additional devtools checks for fda
> > Checking version number has three components... OK
> > Checking dependencies don't rely on dev versions... OK
> > Checking DESCRIPTION doesn't have Remotes field... OK
> > ──
> > Were devtool's checks successful?
> > 1: I forget
> > 2: No
> > 3: Absolutely
> >
> > Selection: 3
> > Have you fixed all existing problems at
> > https://cran.rstudio.com//web/checks/check_results_fda.html ?
> > 1: Yes
> > 2: Not yet
> > 3: No
> >
> > Selection: 1
> > Have you checked on R-hub (with `check_rhub()`)?
> > 1: Not yet
> > 2: I forget
> > 3: Definitely
> >
> > Selection: 3
> > Have you checked on win-builder (with `check_win_devel()`)?
> > 1: No
> > 2: Nope
> > 3: Absolutely
> >
> > Selection: 3
> > Have you checked the 67 reverse dependencies (with the revdepcheck
> package)?
> > 1: Definitely
> > 2: No
> > 3: U... Maybe?
> >
> > Selection: 1
> > Have you updated `NEWS.md` file?
> > 1: U... Maybe?
> > 2: No
> > 3: Yeah
> >
> > Selection: 3
> > Have you updated `DESCRIPTION`?
> > 1: Yup
> > 2: Nope
> > 3: I forget
> >
> > Selection: 1
> > Have you updated `cran-comments.md?`
> > 1: Nope
> > 2: Not yet
> > 3: Yeah
> >
> > Selection: 3
> > ── Running Git checks for fda
> > Current branch: master
> > Checking uncommitted files...
> > WARNING: All files should be tracked and committed before release.
> Please add and commit.
> > Checking synchronisation with remote branch...
> > ERROR: Error in 'git2r_remote_fetch': unsupported URL protocol
> >
> > ──
> > Were Git checks successful?
> > 1: Not yet
> > 2: Nope
> > 3: Yup
> >
> > Selection: 3
> > Is your email address ram...@psych.mcgill.ca?
> > 1: Yup
> > 2: I forget
> > 3: U... Maybe?
> >
> > Selection: 1
> > Building
> > ✓ checking for file
> ‘/Users/jamesramsay/Documents/R/fda_work/fda/DESCRIPTION’ (437ms)
> > ─ preparing ‘fda’: (5.8s)
> > ✓ checking DESCRIPTION meta-information ...
> > ─ checking for LF line-endings in source and make files and shell
> scripts (1.6s)
> > ─ checking for empty or unneeded directories
> > ─ building ‘fda_5.1.7.tar.gz’
> >
> > Submitting file:
> /var/folders/sc/6zzfzqbs5w7dl8q5g18tlqfcgn/T//RtmpbcSyMD/fda_5.1.7.tar.gz
> > File size: 102.9 Mb
> > Ready to submit fda (5.1.7) to CRAN?
> > 1: Not yet
> > 2: Absolutely
> > 3: U... Maybe?
> >
> > Selection: 2
> > Uploading package & comments
> > Confirming submission
> > Error in if (new_url$query$submit == "1") { : argument is of length zero
> > In addition: Warning messages:
> > 1: In charToRaw(enc2utf8(val)) :
> > argument should be a character vector of length 1
> > all but the first element will be ignored
> > 2: In charToRaw(enc2utf8(val)) :
> > argument should be a character vector of length 1
> > all but the first element will be ignored
> >
> >
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-package-devel
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[R-pkg-devel] devtools::release() does not release
Hi folks,
devtools::release() gave the following errors:
...
Ready to submit fda (5.1.7) to CRAN?
1: Not yet
2: Absolutely
3: U... Maybe?
Selection: 2
Uploading package & comments
Confirming submission
Error in if (new_url$query$submit == "1") { : argument is of length zero
In addition: Warning messages:
1: In charToRaw(enc2utf8(val)) :
argument should be a character vector of length 1
all but the first element will be ignored
2: In charToRaw(enc2utf8(val)) :
argument should be a character vector of length 1
all but the first element will be ignored
Jim Ramsay got this after setwd to what seemed to be the appropriate
working directory and then running devtools::release(), as noted above.
As near as both of us can determine, we've followed essentially the same
protocol here as with other package submissions.
In case you want the entire devtools::release() transcript, it
appears below running under Big Sur on a Mac.
Suggestions?
Thanks,
Spencer Graves & Jim Ramsay
——
devtools::release()
Have you checked for spelling errors (with `spell_check()`)?
1: Not yet
2: Nope
3: Absolutely
Selection: 3
Have you run `R CMD check` locally?
1: Yes
2: I forget
3: No
Selection: 1
── Running additional devtools checks for fda
Checking version number has three components... OK
Checking dependencies don't rely on dev versions... OK
Checking DESCRIPTION doesn't have Remotes field... OK
──
Were devtool's checks successful?
1: I forget
2: No
3: Absolutely
Selection: 3
Have you fixed all existing problems at
https://cran.rstudio.com//web/checks/check_results_fda.html ?
1: Yes
2: Not yet
3: No
Selection: 1
Have you checked on R-hub (with `check_rhub()`)?
1: Not yet
2: I forget
3: Definitely
Selection: 3
Have you checked on win-builder (with `check_win_devel()`)?
1: No
2: Nope
3: Absolutely
Selection: 3
Have you checked the 67 reverse dependencies (with the revdepcheck
package)?
1: Definitely
2: No
3: U... Maybe?
Selection: 1
Have you updated `NEWS.md` file?
1: U... Maybe?
2: No
3: Yeah
Selection: 3
Have you updated `DESCRIPTION`?
1: Yup
2: Nope
3: I forget
Selection: 1
Have you updated `cran-comments.md?`
1: Nope
2: Not yet
3: Yeah
Selection: 3
── Running Git checks for fda
Current branch: master
Checking uncommitted files...
WARNING: All files should be tracked and committed before release.
Please add and commit.
Checking synchronisation with remote branch...
ERROR: Error in 'git2r_remote_fetch': unsupported URL protocol
──
Were Git checks successful?
1: Not yet
2: Nope
3: Yup
Selection: 3
Is your email address ram...@psych.mcgill.ca?
1: Yup
2: I forget
3: U... Maybe?
Selection: 1
Building
✓ checking for file
‘/Users/jamesramsay/Documents/R/fda_work/fda/DESCRIPTION’ (437ms)
─ preparing ‘fda’: (5.8s)
✓ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell
scripts (1.6s)
─ checking for empty or unneeded directories
─ building ‘fda_5.1.7.tar.gz’
Submitting file:
/var/folders/sc/6zzfzqbs5w7dl8q5g18tlqfcgn/T//RtmpbcSyMD/fda_5.1.7.tar.gz
File size: 102.9 Mb
Ready to submit fda (5.1.7) to CRAN?
1: Not yet
2: Absolutely
3: U... Maybe?
Selection: 2
Uploading package & comments
Confirming submission
Error in if (new_url$query$submit == "1") { : argument is of length zero
In addition: Warning messages:
1: In charToRaw(enc2utf8(val)) :
argument should be a character vector of length 1
all but the first element will be ignored
2: In charToRaw(enc2utf8(val)) :
argument should be a character vector of length 1
all but the first element will be ignored
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Re: [Bioc-devel] Missing knitcitations package on devel for PharmacoGx
This problem has been recognized:
https://github.com/cboettig/knitcitations/issues/107
In a few days it will likely clear.
On Wed, Nov 25, 2020 at 10:26 PM Eeles, Christopher <
christopher.ee...@uhnresearch.ca> wrote:
> Hello Bioc community,
>
> I am the maintainer for PharmacoGx and have noticed that I have an error
> on all platforms of the devel branch related to the knitcitations package.
>
>
> * checking for file ‘PharmacoGx/DESCRIPTION’ ... OK
> * preparing ‘PharmacoGx’:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> --- re-building ‘CreatingPharmacoSet.Rmd’ using rmarkdown
> Quitting from lines 79-82 (CreatingPharmacoSet.Rmd)
> Error: processing vignette 'CreatingPharmacoSet.Rmd' failed with
> diagnostics:
> there is no package called 'knitcitations'
> --- failed re-building ‘CreatingPharmacoSet.Rmd’
>
> --- re-building ‘PharmacoGx.Rmd’ using rmarkdown
> Quitting from lines 79-82 (PharmacoGx.Rmd)
> Error: processing vignette 'PharmacoGx.Rmd' failed with diagnostics:
> there is no package called 'knitcitations'
> --- failed re-building ‘PharmacoGx.Rmd’
>
> SUMMARY: processing the following files failed:
> ‘CreatingPharmacoSet.Rmd’ ‘PharmacoGx.Rmd’
>
> Error: Vignette re-building failed.
> Execution halted
>
> The package builds fine on the release branch with the same vignettes and
> knitcitations in the suggests field of the description.
>
> Any advice on how I can fix this? It seems like my suggests aren't being
> installed on the devel branch.
>
> Thanks for your assistance.
>
> Best,
> Christopher Eeles
> Software Developer
> Benjamin Haibe-Kains Lab
> Princess Margaret Cancer Centre
>
> This e-mail may contain confidential and/or privileged i...{{dropped:22}}
>
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>
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The information in this e-mail is intended only for the ...{{dropped:18}}
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Re: [Rd] [External] Re: .Internal(quit(...)): system call failed: Cannot allocate memory
Thank you Luke for looking into it. Your knowledge of gc is definitely
helpful here. I put comments inline below.
Best,
Jan
On Wed, Nov 25, 2020 at 10:38 PM wrote:
>
> On Tue, 24 Nov 2020, Jan Gorecki wrote:
>
> > As for other calls to system. I avoid calling system. In the past I
> > had some (to get memory stats from OS), but they were failing with
> > exactly the same issue. So yes, if I would add call to system before
> > calling quit, I believe it would fail with the same error.
> > At the same time I think (although I am not sure) that new allocations
> > made in R are working fine. So R seems to reserve some memory and can
> > continue to operate, while external call like system will fail. Maybe
> > it is like this by design, don't know.
>
> Thanks for the report on quit(). We're exploring how to make the
> cleanup on exit more robust to low memory situations like these.
>
> >
> > Aside from this problem that is easy to report due to the warning
> > message, I think that gc() is choking at the same time. I tried to
> > make reproducible example for that, multiple times but couldn't, let
> > me try one more time.
> > It happens to manifest when there is 4e8+ unique characters/factors in
> > an R session. I am able to reproduce it using data.table and dplyr
> > (0.8.4 because 1.0.0+ fails even sooner), but using base R is not easy
> > because of the size. I described briefly problem in:
> > https://github.com/h2oai/db-benchmark/issues/110
>
> Because of the design of R's character vectors, with each element
> allocated separately, R is never going to be great at handling huge
> numbers of distinct strings. But it can do an adequate job given
> enough memory to work with.
>
> When I run your GitHub issue example on a machine with around 500 Gb
> of RAM it seems to run OK; /usr/bin/time reports
>
> 2706.89user 161.89system 37:10.65elapsed 128%CPU (0avgtext+0avgdata
> 92180796maxresident)k
> 0inputs+103450552outputs (0major+38716351minor)pagefaults 0swaps
>
> So the memory footprint is quite large. Using gc.time() it looks like
> about 1/3 of the time is in GC. Not ideal, and maybe could be improved
> on a bit, but probably not by much. The GC is basically doing an
> adequate job, given enough RAM.
Agree, 1/3 is a lot but still acceptable. So this strictly is not
something that requires intervention.
PS. I wasn't aware of gc.time(), it may be worth linking it from
SeeAlso in gc() manual.
>
> If you run this example on a system without enough RAM, or with other
> programs competing for RAM, you are likely to end up fighting with
> your OS/hardware's virtual memory system. When I try to run it on a
> 16Gb system it churns for an hour or so before getting killed, and
> /usr/bin/time reports a huge number of page faults:
>
> 312523816inputs+0outputs (24761285major+25762068minor)pagefaults 0swaps
>
> You are probably experiencing something similar.
Yes, this is exactly what I am experiencing.
The machine is a bare metal machine of 128GB mem, csv size 50GB,
data.frame size 74GB.
In my case it churns for ~3h before it gets killed with SIGINT from
the parent R process which uses 3h as a timeout for this script.
This is something I would like to be addressed because gc time is far
bigger than actual computation time. This is not really acceptable, I
would prefer to raise an exception instead.
>
> There may be opportunities for more tuning of the GC to better handle
> running this close to memory limits, but I doubt the payoff would be
> worth the effort.
If you don't have plans/time to work on that anytime soon, then I can
fill bugzilla for this problem so it won't get lost in the mailing
list.
>
> Best,
>
> luke
>
> > It would help if gcinfo() could take FALSE/TRUE/2L where 2L will print
> > even more information about gc, like how much time the each gc()
> > process took, how many objects it has to check on each level.
> >
> > Best regards,
> > Jan
> >
> >
> >
> > On Tue, Nov 24, 2020 at 1:05 PM Tomas Kalibera
> > wrote:
> >>
> >> On 11/24/20 11:27 AM, Jan Gorecki wrote:
> >>> Thanks Bill for checking that.
> >>> It was my impression that warnings are raised from some internal
> >>> system calls made when quitting R. At that point I don't have much
> >>> control over checking the return status of those.
> >>> Your suggestion looks good to me.
> >>>
> >>> Tomas, do you think this could help? could this be implemented?
> >>
> >> I think this is a good suggestion. Deleting files on Unix was changed
> >> from system("rm") to doing that in C, and deleting the session directory
> >> should follow.
> >>
> >> It might also help diagnosing your problem, but I don't think it would
> >> solve it. If the diagnostics in R works fine and the OS was so
> >> hopelessly out of memory that it couldn't run any more external
> >> processes, then really this is not a problem of R, but of having
> >> exhausted the resources. And it would be a coincidence that just this
> >> particular call to "system" at the end of the
Re: [Bioc-devel] Missing knitcitations package on devel for PharmacoGx
Hi Christopher,
It looks like the knitcitations package is no longer on CRAN. Heading to
https://cran.r-project.org/web/packages/knitcitations/index.html results in:
Package ‘knitcitations’ was removed from the CRAN repository.
Formerly available versions can be obtained from the archive.
Archived on 2020-10-27 as reauired archived package 'RefManageR'.
My guess is the release branch has a copy of knitcitations installed from
before it was removed from CRAN, so you don't see the error, but a fresh R
installation using either release or devel would throw the same problem.
The latest commit message to https://github.com/cboettig/knitcitations is
'prep for release', so it looks likely that the author of knitcitations is
addressing the CRAN issue. I would hang tight for a while longer and hope
it gets smoothed out there.
Mike
On Thu, 26 Nov 2020 at 04:26, Eeles, Christopher <
christopher.ee...@uhnresearch.ca> wrote:
> Hello Bioc community,
>
> I am the maintainer for PharmacoGx and have noticed that I have an error
> on all platforms of the devel branch related to the knitcitations package.
>
>
> * checking for file ‘PharmacoGx/DESCRIPTION’ ... OK
> * preparing ‘PharmacoGx’:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> --- re-building ‘CreatingPharmacoSet.Rmd’ using rmarkdown
> Quitting from lines 79-82 (CreatingPharmacoSet.Rmd)
> Error: processing vignette 'CreatingPharmacoSet.Rmd' failed with
> diagnostics:
> there is no package called 'knitcitations'
> --- failed re-building ‘CreatingPharmacoSet.Rmd’
>
> --- re-building ‘PharmacoGx.Rmd’ using rmarkdown
> Quitting from lines 79-82 (PharmacoGx.Rmd)
> Error: processing vignette 'PharmacoGx.Rmd' failed with diagnostics:
> there is no package called 'knitcitations'
> --- failed re-building ‘PharmacoGx.Rmd’
>
> SUMMARY: processing the following files failed:
> ‘CreatingPharmacoSet.Rmd’ ‘PharmacoGx.Rmd’
>
> Error: Vignette re-building failed.
> Execution halted
>
> The package builds fine on the release branch with the same vignettes and
> knitcitations in the suggests field of the description.
>
> Any advice on how I can fix this? It seems like my suggests aren't being
> installed on the devel branch.
>
> Thanks for your assistance.
>
> Best,
> Christopher Eeles
> Software Developer
> Benjamin Haibe-Kains Lab
> Princess Margaret Cancer Centre
>
> This e-mail may contain confidential and/or privileged i...{{dropped:22}}
>
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