Re: [Bioc-devel] Regarding BioC devel build of package surfaltr
On 12/10/2021 14:24, Hervé Pagès wrote: Probably the build/ folder that doesn't belong to a package source tree. You removed it today (commit 546e727eb21be2f1da8cd063f431a227345847da) but that was after the builds started so this will only be reflected on Wednesday's build report. I meant on Thursday's build report, sorry. H. Best, H. On 12/10/2021 06:50, Pooja Gangras wrote: Hi all, My package just got accepted and was added to the nightly build on Friday. The build report shows error in installation which it did not show earlier during package submission ( pkg submission issue here surfaltr · Issue #2256 · Bioconductor/Contributions (github.com)) This is the current build (Multiple platform build/check report for BioC 3.14 - All results for package surfaltr (bioconductor.org)) error: ** installing vignettes Warning in file(con, "w") : cannot open file '/home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-surfaltr/00new/surfaltr/doc/index.html': No such file or directory Error in file(con, "w") : cannot open the connection ERROR: installing vignettes failed * removing ‘/home/biocbuild/bbs-3.14-bioc/R/library/surfaltr’ There are several different solutions suggested in this stackoverflow page (r - Installing package fails when building vignettes ((..)/doc/index.html is missing) - Stack Overflow) . I do have ‘inst/doc’ in my .gitignore file and was wondering if I need to remove it to fix this build issue or is there something else I need to fix? Thank you, Pooja P.S. I have tried sending this email a few times using the email address linked to my package but for some reason the email is not posted to the mailing list and I get a response that says 'The message's content type was not explicitly allowed' [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Strange "internal logical NA value has been modified" error
Thanks, Martin and Henrik!
My previous confusing reply from a few minutes ago was due my university
GMail hiding your replies in All Mail.
I'll consider both your suggestions carefully and thank you again for
the quick and thoughtful replies.
Pairksheet
On 10/12/21 8:03 PM, Henrik Bengtsson wrote:
*Message sent from a system outside of UConn.*
In addition to checking with Valgrind, the ASan/UBsan and rchk
platforms on R-Hub (https://builder.r-hub.io/) can probably also be
useful;
rhub::check(platform = "linux-x86_64-rocker-gcc-san")
rhub::check(platform = "ubuntu-rchk")
/Henrik
On Tue, Oct 12, 2021 at 4:54 PM Martin Morgan wrote:
It is from base R
https://github.com/wch/r-source/blob/a984cc29b9b8d8821f8eb2a1081d9e0d1d4df56e/src/main/memory.c#L3214
and likely indicates memory corruption, not necessarily in the code that
triggers the error (this is when the garbage collector is triggered...).
Probably in *your* C code :) since it's the least tested. Probably writing out
of bounds.
This could be quite tricky to debug. I'd try to get something close to a
minimal reproducible example.
I'd try to take devtools out of the picture, maybe running the test/testhat.R
script from the command line using Rscript, or worst case creating a shell
package that adds minimal code and can be checked with R CMD build
--no-build-vignettes / R CMD check.
You could try inserting gc() before / after the unit test; it might make it
clear that the unit test isn't the problem. You could also try gctorture(TRUE);
this will make your code run extremely painfully slowly, which puts a big
premium on having a minimal reproducible example; you could put this near the
code chunks that are causing problems.
You might have success running under valgrind, something like R -d valgrind -f
minimal_script.R.
Hope those suggestions help!
Martin
On 10/12/21, 6:43 PM, "Bioc-devel on behalf of Pariksheet Nanda"
wrote:
Hi folks,
I've been told to ask some of my more fun questions on this mailing list
instead of Slack. I'm climbing the ladder of submitting my first
Bioconductor package (https://gitlab.com/coregenomics/tsshmm) and feel
like there are gremlins that keep adding rungs to the top of the ladder.
The latest head scratcher from running devtools::check() is a unit
test for a trivial 2 line function failing with this gem of an error:
> test_check("tsshmm")
══ Failed tests
── Error (test-tss.R:11:5): replace_unstranded splits unstranded into +
and - ──
Error in `tryCatchOne(expr, names, parentenv, handlers[[1L]])`: internal
logical NA value has been modified
Backtrace:
█
1. ├─testthat::expect_equal(...) test-tss.R:11:4
2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg =
"expected")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─GenomicRanges::GRanges(c("chr:100:+", "chr:100:-"))
5. └─methods::as(seqnames, "GRanges")
6. └─GenomicRanges:::asMethod(object)
7. └─GenomicRanges::GRanges(ans_seqnames, ans_ranges, ans_strand)
8. └─GenomicRanges:::new_GRanges(...)
9. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len)
10. └─S4Vectors::make_zero_col_DFrame(x_len)
11. └─S4Vectors::new2("DFrame", nrows = nrow, check =
FALSE)
12. └─methods::new(...)
13. ├─methods::initialize(value, ...)
14. └─methods::initialize(value, ...)
15. └─methods::validObject(.Object)
16. └─base::try(...)
17. └─base::tryCatch(...)
18. └─base:::tryCatchList(expr, classes,
parentenv, handlers)
19. └─base:::tryCatchOne(expr, names,
parentenv, handlers[[1L]])
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 109 ]
The full continuous integration log is here:
https://gitlab.com/coregenomics/tsshmm/-/jobs/1673603868
The function in question is:
replace_unstranded <- function (gr) {
idx <- strand(gr) == "*"
if (length(idx) == 0L)
return(gr)
sort(c(
gr[! idx],
`strand<-`(gr[idx], value = "+"),
`strand<-`(gr[idx], value = "-")))
}
Also online here:
https://gitlab.com/coregenomics/tsshmm/-/blob/ef5e19a0e2f68fca93665bc417afbcfb6d437189/R/hmm.R#L170-178
... and the unit test is:
test_that("replace_unstranded splits unstranded into + and -", {
expect_equal(replace_unstranded(GRanges("chr:100")),
GRanges(c("chr:100:+", "chr:100:-")))
expect_equal(replace_unstranded(GRanges(c("chr:100", "chr:200:+"))),
Re: [Bioc-devel] Strange "internal logical NA value has been modified" error
Hi all, On 10/12/21 6:43 PM, Pariksheet Nanda wrote: Error in `...`: internal logical NA value has been modified In the R source code, this error is in src/main/memory.c so I was thinking one way of investigating might be to run `R --debugger gdb`, then running R to load the symbols and either: 1) set a breakpoint for when it reaches that particular line in memory.c:R_gc_internal and then walk up the stack, 2) or set a watch point on memory.c:R_gc_internal:R_LogicalNAValue (somehow; having trouble getting gdb to reach that context). 3) Then I thought, maybe this is getting far into the weeds and instead I could check the most common C related error by enabling bounds checking of my C arrays per section 4.4 of the R-exts manual: $ R -q > options(CBoundsCheck = TRUE) > Sys.setenv(R_C_BOUNDS_CHECK = "yes") # Try both ways *shrug* > devtools::test() ... # All tests still pass. > devtools::check() ... # No change :( Maybe I'm not sure I'm using that option correctly? Or the option is ignored in devtools::check(). Or indeed, the error is not from over running C array boundaries. It turns out that using the precompiled debug symbols[1] isn't all that useful here because I don't get line numbers in gdb without the source files and many symbols are optimized out, so it looks like I would need to compile R from source with -ggdb first instead of using the Debian packages. Hopefully this is still the right approach? Pariksheet [1] After install r-base-core-dbg on Debian for the debug symbols. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Strange "internal logical NA value has been modified" error
In addition to checking with Valgrind, the ASan/UBsan and rchk
platforms on R-Hub (https://builder.r-hub.io/) can probably also be
useful;
> rhub::check(platform = "linux-x86_64-rocker-gcc-san")
> rhub::check(platform = "ubuntu-rchk")
/Henrik
On Tue, Oct 12, 2021 at 4:54 PM Martin Morgan wrote:
>
> It is from base R
>
>
> https://github.com/wch/r-source/blob/a984cc29b9b8d8821f8eb2a1081d9e0d1d4df56e/src/main/memory.c#L3214
>
> and likely indicates memory corruption, not necessarily in the code that
> triggers the error (this is when the garbage collector is triggered...).
> Probably in *your* C code :) since it's the least tested. Probably writing
> out of bounds.
>
> This could be quite tricky to debug. I'd try to get something close to a
> minimal reproducible example.
>
> I'd try to take devtools out of the picture, maybe running the test/testhat.R
> script from the command line using Rscript, or worst case creating a shell
> package that adds minimal code and can be checked with R CMD build
> --no-build-vignettes / R CMD check.
>
> You could try inserting gc() before / after the unit test; it might make it
> clear that the unit test isn't the problem. You could also try
> gctorture(TRUE); this will make your code run extremely painfully slowly,
> which puts a big premium on having a minimal reproducible example; you could
> put this near the code chunks that are causing problems.
>
> You might have success running under valgrind, something like R -d valgrind
> -f minimal_script.R.
>
> Hope those suggestions help!
>
> Martin
>
>
> On 10/12/21, 6:43 PM, "Bioc-devel on behalf of Pariksheet Nanda"
>
> wrote:
>
> Hi folks,
>
> I've been told to ask some of my more fun questions on this mailing list
> instead of Slack. I'm climbing the ladder of submitting my first
> Bioconductor package (https://gitlab.com/coregenomics/tsshmm) and feel
> like there are gremlins that keep adding rungs to the top of the ladder.
> The latest head scratcher from running devtools::check() is a unit
> test for a trivial 2 line function failing with this gem of an error:
>
>
> > test_check("tsshmm")
> ══ Failed tests
>
> ── Error (test-tss.R:11:5): replace_unstranded splits unstranded into +
> and - ──
> Error in `tryCatchOne(expr, names, parentenv, handlers[[1L]])`: internal
> logical NA value has been modified
> Backtrace:
> █
>1. ├─testthat::expect_equal(...) test-tss.R:11:4
>2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg =
> "expected")
>3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
>4. └─GenomicRanges::GRanges(c("chr:100:+", "chr:100:-"))
>5. └─methods::as(seqnames, "GRanges")
>6. └─GenomicRanges:::asMethod(object)
>7. └─GenomicRanges::GRanges(ans_seqnames, ans_ranges, ans_strand)
>8. └─GenomicRanges:::new_GRanges(...)
>9. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len)
> 10. └─S4Vectors::make_zero_col_DFrame(x_len)
> 11. └─S4Vectors::new2("DFrame", nrows = nrow, check =
> FALSE)
> 12. └─methods::new(...)
> 13. ├─methods::initialize(value, ...)
> 14. └─methods::initialize(value, ...)
> 15. └─methods::validObject(.Object)
> 16. └─base::try(...)
> 17. └─base::tryCatch(...)
> 18. └─base:::tryCatchList(expr, classes,
> parentenv, handlers)
> 19. └─base:::tryCatchOne(expr, names,
> parentenv, handlers[[1L]])
> [ FAIL 1 | WARN 0 | SKIP 0 | PASS 109 ]
>
>
> The full continuous integration log is here:
> https://gitlab.com/coregenomics/tsshmm/-/jobs/1673603868
>
> The function in question is:
>
>
> replace_unstranded <- function (gr) {
> idx <- strand(gr) == "*"
> if (length(idx) == 0L)
> return(gr)
> sort(c(
> gr[! idx],
> `strand<-`(gr[idx], value = "+"),
> `strand<-`(gr[idx], value = "-")))
> }
>
>
> Also online here:
>
> https://gitlab.com/coregenomics/tsshmm/-/blob/ef5e19a0e2f68fca93665bc417afbcfb6d437189/R/hmm.R#L170-178
>
> ... and the unit test is:
>
>
> test_that("replace_unstranded splits unstranded into + and -", {
> expect_equal(replace_unstranded(GRanges("chr:100")),
> GRanges(c("chr:100:+", "chr:100:-")))
> expect_equal(replace_unstranded(GRanges(c("chr:100", "chr:200:+"))),
> sort(GRanges(c("chr:100:+", "chr:100:-", "chr:200:+"
> })
>
>
> Also online here:
>
>
Re: [Bioc-devel] Windows-specific Function Not Found Error
Hello, Ah, I had a few different uses of MultiAssayExperiment::colData in a particular function of the package, but one line had only colData without the scoping in front. I wish that R error messages displayed R file names and line numbers more often. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Strange "internal logical NA value has been modified" error
It is from base R
https://github.com/wch/r-source/blob/a984cc29b9b8d8821f8eb2a1081d9e0d1d4df56e/src/main/memory.c#L3214
and likely indicates memory corruption, not necessarily in the code that
triggers the error (this is when the garbage collector is triggered...).
Probably in *your* C code :) since it's the least tested. Probably writing out
of bounds.
This could be quite tricky to debug. I'd try to get something close to a
minimal reproducible example.
I'd try to take devtools out of the picture, maybe running the test/testhat.R
script from the command line using Rscript, or worst case creating a shell
package that adds minimal code and can be checked with R CMD build
--no-build-vignettes / R CMD check.
You could try inserting gc() before / after the unit test; it might make it
clear that the unit test isn't the problem. You could also try gctorture(TRUE);
this will make your code run extremely painfully slowly, which puts a big
premium on having a minimal reproducible example; you could put this near the
code chunks that are causing problems.
You might have success running under valgrind, something like R -d valgrind -f
minimal_script.R.
Hope those suggestions help!
Martin
On 10/12/21, 6:43 PM, "Bioc-devel on behalf of Pariksheet Nanda"
wrote:
Hi folks,
I've been told to ask some of my more fun questions on this mailing list
instead of Slack. I'm climbing the ladder of submitting my first
Bioconductor package (https://gitlab.com/coregenomics/tsshmm) and feel
like there are gremlins that keep adding rungs to the top of the ladder.
The latest head scratcher from running devtools::check() is a unit
test for a trivial 2 line function failing with this gem of an error:
> test_check("tsshmm")
══ Failed tests
── Error (test-tss.R:11:5): replace_unstranded splits unstranded into +
and - ──
Error in `tryCatchOne(expr, names, parentenv, handlers[[1L]])`: internal
logical NA value has been modified
Backtrace:
█
1. ├─testthat::expect_equal(...) test-tss.R:11:4
2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg =
"expected")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─GenomicRanges::GRanges(c("chr:100:+", "chr:100:-"))
5. └─methods::as(seqnames, "GRanges")
6. └─GenomicRanges:::asMethod(object)
7. └─GenomicRanges::GRanges(ans_seqnames, ans_ranges, ans_strand)
8. └─GenomicRanges:::new_GRanges(...)
9. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len)
10. └─S4Vectors::make_zero_col_DFrame(x_len)
11. └─S4Vectors::new2("DFrame", nrows = nrow, check = FALSE)
12. └─methods::new(...)
13. ├─methods::initialize(value, ...)
14. └─methods::initialize(value, ...)
15. └─methods::validObject(.Object)
16. └─base::try(...)
17. └─base::tryCatch(...)
18. └─base:::tryCatchList(expr, classes,
parentenv, handlers)
19. └─base:::tryCatchOne(expr, names,
parentenv, handlers[[1L]])
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 109 ]
The full continuous integration log is here:
https://gitlab.com/coregenomics/tsshmm/-/jobs/1673603868
The function in question is:
replace_unstranded <- function (gr) {
idx <- strand(gr) == "*"
if (length(idx) == 0L)
return(gr)
sort(c(
gr[! idx],
`strand<-`(gr[idx], value = "+"),
`strand<-`(gr[idx], value = "-")))
}
Also online here:
https://gitlab.com/coregenomics/tsshmm/-/blob/ef5e19a0e2f68fca93665bc417afbcfb6d437189/R/hmm.R#L170-178
... and the unit test is:
test_that("replace_unstranded splits unstranded into + and -", {
expect_equal(replace_unstranded(GRanges("chr:100")),
GRanges(c("chr:100:+", "chr:100:-")))
expect_equal(replace_unstranded(GRanges(c("chr:100", "chr:200:+"))),
sort(GRanges(c("chr:100:+", "chr:100:-", "chr:200:+"
})
Also online here:
https://gitlab.com/coregenomics/tsshmm/-/blob/ef5e19a0e2f68fca93665bc417afbcfb6d437189/tests/testthat/test-tss.R#L11-L12
What's interesting is this is *not* reproducible by running
devtools::test() but only devtools::check() so as far as I know there
isn't a way to interactively debug this while devtools::check() is going on?
Every few days I've seen on that "internal ... value has been modified"
which prevents me from running nearly any R commands. Originally I
would restart R, but then I found I could clear that error by running
gc(). No idea what causes it. Maybe
Re: [Bioc-devel] Windows-specific Function Not Found Error
Remember that Windows doesn�t have �forked� parallelism; all processes are
running in separate processes where the functions in use need to be made
explicitly available.
Likely you can emulate this error on non-windows by using �SnowParam()� instead
of MulticoreParam(), e.g.,
> library(SummarizedExperiment)
> library(BiocParallel)
> result <- bplapply(1:2, function(i) colData, BPPARAM = MulticoreParam(2))
> result <- bplapply(1:2, function(i) colData, BPPARAM = SnowParam(2))
Error: BiocParallel errors
2 remote errors, element index: 1, 2
0 unevaluated and other errors
first remote error: object 'colData' not found
Solve the problem by explicitly indicating the source of the function
> result <- bplapply(1:2, function(i) SummarizedExperiment::colData, BPPARAM =
> SnowParam(2))
or perhaps something along the lines of
FUN = function(i) {
library(SummarizedExperiment)
colData
}
I would guess that your package Depends: but does not Import the package where
colData is defined; I think BiocParallel would normally serialize the package
environment, and hence colData, to the worker�
Martin
On 10/12/21, 7:00 PM, "Bioc-devel" wrote:
Good day,
I see a checking failure for ClassifyR for Windows Server 2019 only. The error
is
Error: BiocParallel errors
4 remote errors, element index: 1, 4, 6, 8
6 unevaluated and other errors
first remote error: could not find function "colData"
Is there anything I can change in my code to help it pass? The error doesn't
appear on the two other Bioconductor servers.
--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
___
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
[Bioc-devel] Windows-specific Function Not Found Error
Good day, I see a checking failure for ClassifyR for Windows Server 2019 only. The error is Error: BiocParallel errors 4 remote errors, element index: 1, 4, 6, 8 6 unevaluated and other errors first remote error: could not find function "colData" Is there anything I can change in my code to help it pass? The error doesn't appear on the two other Bioconductor servers. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Strange "internal logical NA value has been modified" error
Hi folks,
I've been told to ask some of my more fun questions on this mailing list
instead of Slack. I'm climbing the ladder of submitting my first
Bioconductor package (https://gitlab.com/coregenomics/tsshmm) and feel
like there are gremlins that keep adding rungs to the top of the ladder.
The latest head scratcher from running devtools::check() is a unit
test for a trivial 2 line function failing with this gem of an error:
> test_check("tsshmm")
══ Failed tests
── Error (test-tss.R:11:5): replace_unstranded splits unstranded into +
and - ──
Error in `tryCatchOne(expr, names, parentenv, handlers[[1L]])`: internal
logical NA value has been modified
Backtrace:
█
1. ├─testthat::expect_equal(...) test-tss.R:11:4
2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg =
"expected")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─GenomicRanges::GRanges(c("chr:100:+", "chr:100:-"))
5. └─methods::as(seqnames, "GRanges")
6. └─GenomicRanges:::asMethod(object)
7. └─GenomicRanges::GRanges(ans_seqnames, ans_ranges, ans_strand)
8. └─GenomicRanges:::new_GRanges(...)
9. └─S4Vectors:::normarg_mcols(mcols, Class, ans_len)
10. └─S4Vectors::make_zero_col_DFrame(x_len)
11. └─S4Vectors::new2("DFrame", nrows = nrow, check = FALSE)
12. └─methods::new(...)
13. ├─methods::initialize(value, ...)
14. └─methods::initialize(value, ...)
15. └─methods::validObject(.Object)
16. └─base::try(...)
17. └─base::tryCatch(...)
18. └─base:::tryCatchList(expr, classes,
parentenv, handlers)
19. └─base:::tryCatchOne(expr, names,
parentenv, handlers[[1L]])
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 109 ]
The full continuous integration log is here:
https://gitlab.com/coregenomics/tsshmm/-/jobs/1673603868
The function in question is:
replace_unstranded <- function (gr) {
idx <- strand(gr) == "*"
if (length(idx) == 0L)
return(gr)
sort(c(
gr[! idx],
`strand<-`(gr[idx], value = "+"),
`strand<-`(gr[idx], value = "-")))
}
Also online here:
https://gitlab.com/coregenomics/tsshmm/-/blob/ef5e19a0e2f68fca93665bc417afbcfb6d437189/R/hmm.R#L170-178
... and the unit test is:
test_that("replace_unstranded splits unstranded into + and -", {
expect_equal(replace_unstranded(GRanges("chr:100")),
GRanges(c("chr:100:+", "chr:100:-")))
expect_equal(replace_unstranded(GRanges(c("chr:100", "chr:200:+"))),
sort(GRanges(c("chr:100:+", "chr:100:-", "chr:200:+"
})
Also online here:
https://gitlab.com/coregenomics/tsshmm/-/blob/ef5e19a0e2f68fca93665bc417afbcfb6d437189/tests/testthat/test-tss.R#L11-L12
What's interesting is this is *not* reproducible by running
devtools::test() but only devtools::check() so as far as I know there
isn't a way to interactively debug this while devtools::check() is going on?
Every few days I've seen on that "internal ... value has been modified"
which prevents me from running nearly any R commands. Originally I
would restart R, but then I found I could clear that error by running
gc(). No idea what causes it. Maybe some S4 magic?
Yes, I have downloaded the mailing lists for bioc-devel, r-devel,
r-help, and r-package-devel and see no mention of "value has been
modified" [1].
Any help appreciated.
Pariksheet
[1] Mailing lists downloader:
#!/bin/bash -x
for url in
https://stat.ethz.ch/pipermail/{bioc-devel,r-{devel,help,package-devel}}/
do
dir=$(basename $url)
wget \
--timestamping \
--no-remove-listing \
--recursive \
--level 1 \
--no-directories \
--no-host-directories \
--cut-dirs 2 \
--directory-prefix "$dir" \
--accept '*.txt.gz' \
--relative \
--no-parent \
$url
done
___
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Re: [Bioc-devel] Regarding BioC devel build of package surfaltr
Probably the build/ folder that doesn't belong to a package source tree. You removed it today (commit 546e727eb21be2f1da8cd063f431a227345847da) but that was after the builds started so this will only be reflected on Wednesday's build report. Best, H. On 12/10/2021 06:50, Pooja Gangras wrote: Hi all, My package just got accepted and was added to the nightly build on Friday. The build report shows error in installation which it did not show earlier during package submission ( pkg submission issue here surfaltr · Issue #2256 · Bioconductor/Contributions (github.com)) This is the current build (Multiple platform build/check report for BioC 3.14 - All results for package surfaltr (bioconductor.org)) error: ** installing vignettes Warning in file(con, "w") : cannot open file '/home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-surfaltr/00new/surfaltr/doc/index.html': No such file or directory Error in file(con, "w") : cannot open the connection ERROR: installing vignettes failed * removing ‘/home/biocbuild/bbs-3.14-bioc/R/library/surfaltr’ There are several different solutions suggested in this stackoverflow page (r - Installing package fails when building vignettes ((..)/doc/index.html is missing) - Stack Overflow) . I do have ‘inst/doc’ in my .gitignore file and was wondering if I need to remove it to fix this build issue or is there something else I need to fix? Thank you, Pooja P.S. I have tried sending this email a few times using the email address linked to my package but for some reason the email is not posted to the mailing list and I get a response that says 'The message's content type was not explicitly allowed' [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Regarding BioC devel build of package surfaltr
Probably the build/ folder that doesn't belong to a package source tree. You removed it today (commit 546e727eb21be2f1da8cd063f431a227345847da) but that was after the builds started so this will only be reflected on Wednesday's build report. Best, H. On 12/10/2021 06:50, Pooja Gangras wrote: Hi all, My package just got accepted and was added to the nightly build on Friday. The build report shows error in installation which it did not show earlier during package submission ( pkg submission issue here surfaltr · Issue #2256 · Bioconductor/Contributions (github.com)) This is the current build (Multiple platform build/check report for BioC 3.14 - All results for package surfaltr (bioconductor.org)) error: ** installing vignettes Warning in file(con, "w") : cannot open file '/home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-surfaltr/00new/surfaltr/doc/index.html': No such file or directory Error in file(con, "w") : cannot open the connection ERROR: installing vignettes failed * removing ‘/home/biocbuild/bbs-3.14-bioc/R/library/surfaltr’ There are several different solutions suggested in this stackoverflow page (r - Installing package fails when building vignettes ((..)/doc/index.html is missing) - Stack Overflow) . I do have ‘inst/doc’ in my .gitignore file and was wondering if I need to remove it to fix this build issue or is there something else I need to fix? Thank you, Pooja P.S. I have tried sending this email a few times using the email address linked to my package but for some reason the email is not posted to the mailing list and I get a response that says 'The message's content type was not explicitly allowed' [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Bioconductor Core Team hpages.on.git...@gmail.com ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Failed to locate any version of JAGS version 4
Thank you so much, Herve! It makes sense to me now. I imported R2jags in my
package, which depends on rjags.
Regards,
Zhi Yang
On Tue, Oct 12, 2021 at 1:14 PM Hervé Pagès
wrote:
> Hmm.. so a new version of rjags (4-11) got published on CRAN on Sept 24:
>
>https://cran.r-project.org/package=rjags
>
> and for some reason they modified the code they use in their onLoad()
> hook to find JAGS on Windows. They were using in rjags 4-10:
>
> readRegistry("SOFTWARE\\JAGS", hive="HLM", maxdepth=2, view="32-bit")
>
>
> which was working fine on our Windows server riesling1 (and AFAIK also
> on the CRAN Windows build machine), but in rjags 4-11 they use:
>
> readRegistry("SOFTWARE\\JAGS", hive="HLM", maxdepth=2, view="64-bit")
>
>
>
> which fails on riesling1 with:
>
> Error in readRegistry("SOFTWARE\\JAGS", hive = "HLM", maxdepth = 2,
> view = "64-bit") :
>
>Registry key 'SOFTWARE\JAGS' not found
>
>
> I've reinstalled JAGS-4.3.0 on riesling1 but that doesn't change anything.
>
> Unfortunately this breaks all packages that depend on rjags:
>
>- https://bioconductor.org/checkResults/3.14/bioc-LATEST/CNVrd2/
>- https://bioconductor.org/checkResults/3.14/bioc-LATEST/HiLDA/
>- https://bioconductor.org/checkResults/3.14/bioc-LATEST/infercnv/
>- https://bioconductor.org/checkResults/3.14/bioc-LATEST/MADSEQ/
>
> Help appreciated.
>
> BTW your package HiLDA is one of them so I wonder why rjags is not
> listed in the Imports field.
>
> Best,
> H.
>
>
> On 11/10/2021 21:24, Zhi Yang wrote:
> > Hello everyone,
> >
> > I encountered a problem with two of my Bioconductor packages built on the
> > windows server for the next release. Specifically, it couldn't locate any
> > version of JAGS version 4. Has anyone experienced the same issue with
> > importing or depending on rjags? Thank you!
> >
> > ** using staged installation
> > ** libs
> > "C:/rtools40/mingw32/bin/"g++ -std=gnu++11
> > -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG
> > -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'
> > -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2
> > -mstackrealign -c EMalgorithm.cpp -o EMalgorithm.o
> > "C:/rtools40/mingw32/bin/"g++ -std=gnu++11
> > -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG
> > -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'
> > -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2
> > -mstackrealign -c RcppExports.cpp -o RcppExports.o
> > "C:/rtools40/mingw32/bin/"g++ -std=gnu++11
> > -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG
> > -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'
> > -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2
> > -mstackrealign -c checkBoundary.cpp -o checkBoundary.o
> > "C:/rtools40/mingw32/bin/"g++ -std=gnu++11
> > -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG
> > -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'
> > -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2
> > -mstackrealign -c convertFromToVector.cpp -o convertFromToVector.o
> > C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o
> > HiLDA.dll tmp.def EMalgorithm.o RcppExports.o checkBoundary.o
> > convertFromToVector.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib
> > -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
> > installing to
> D:/biocbuild/bbs-3.14-bioc/meat/HiLDA.buildbin-libdir/00LOCK-HiLDA/00new/HiLDA/libs/i386
> > ** R
> > ** inst
> > ** byte-compile and prepare package for lazy loading
> > Error: .onLoad failed in loadNamespace() for 'rjags', details:
> >call: fun(libname, pkgname)
> >error: Failed to locate any version of JAGS version 4
> >
> > The rjags package is just an interface to the JAGS library
> > Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0)
> > fromhttp://www.sourceforge.net/projects/mcmc-jags/files
> > Execution halted
> > ERROR: lazy loading failed for package 'HiLDA'
> > * removing 'D:/biocbuild/bbs-3.14-bioc/meat/HiLDA.buildbin-libdir/HiLDA'
> >
> >
> > Regards,
> > Zhi Yang
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>
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Re: [Bioc-devel] Failed to locate any version of JAGS version 4
Hmm.. so a new version of rjags (4-11) got published on CRAN on Sept 24:
https://cran.r-project.org/package=rjags
and for some reason they modified the code they use in their onLoad()
hook to find JAGS on Windows. They were using in rjags 4-10:
readRegistry("SOFTWARE\\JAGS", hive="HLM", maxdepth=2, view="32-bit")
which was working fine on our Windows server riesling1 (and AFAIK also
on the CRAN Windows build machine), but in rjags 4-11 they use:
readRegistry("SOFTWARE\\JAGS", hive="HLM", maxdepth=2, view="64-bit")
which fails on riesling1 with:
Error in readRegistry("SOFTWARE\\JAGS", hive = "HLM", maxdepth = 2,
view = "64-bit") :
Registry key 'SOFTWARE\JAGS' not found
I've reinstalled JAGS-4.3.0 on riesling1 but that doesn't change anything.
Unfortunately this breaks all packages that depend on rjags:
- https://bioconductor.org/checkResults/3.14/bioc-LATEST/CNVrd2/
- https://bioconductor.org/checkResults/3.14/bioc-LATEST/HiLDA/
- https://bioconductor.org/checkResults/3.14/bioc-LATEST/infercnv/
- https://bioconductor.org/checkResults/3.14/bioc-LATEST/MADSEQ/
Help appreciated.
BTW your package HiLDA is one of them so I wonder why rjags is not
listed in the Imports field.
Best,
H.
On 11/10/2021 21:24, Zhi Yang wrote:
Hello everyone,
I encountered a problem with two of my Bioconductor packages built on the
windows server for the next release. Specifically, it couldn't locate any
version of JAGS version 4. Has anyone experienced the same issue with
importing or depending on rjags? Thank you!
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11
-I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG
-I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'
-I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2
-mstackrealign -c EMalgorithm.cpp -o EMalgorithm.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11
-I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG
-I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'
-I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2
-mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11
-I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG
-I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'
-I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2
-mstackrealign -c checkBoundary.cpp -o checkBoundary.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11
-I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG
-I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'
-I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2
-mstackrealign -c convertFromToVector.cpp -o convertFromToVector.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o
HiLDA.dll tmp.def EMalgorithm.o RcppExports.o checkBoundary.o
convertFromToVector.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib
-LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to
D:/biocbuild/bbs-3.14-bioc/meat/HiLDA.buildbin-libdir/00LOCK-HiLDA/00new/HiLDA/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Error: .onLoad failed in loadNamespace() for 'rjags', details:
call: fun(libname, pkgname)
error: Failed to locate any version of JAGS version 4
The rjags package is just an interface to the JAGS library
Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0)
fromhttp://www.sourceforge.net/projects/mcmc-jags/files
Execution halted
ERROR: lazy loading failed for package 'HiLDA'
* removing 'D:/biocbuild/bbs-3.14-bioc/meat/HiLDA.buildbin-libdir/HiLDA'
Regards,
Zhi Yang
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--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
___
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[Bioc-devel] Regarding BioC devel build of package surfaltr
Hi all, My package just got accepted and was added to the nightly build on Friday. The build report shows error in installation which it did not show earlier during package submission ( pkg submission issue here surfaltr · Issue #2256 · Bioconductor/Contributions (github.com)) This is the current build (Multiple platform build/check report for BioC 3.14 - All results for package surfaltr (bioconductor.org)) error: ** installing vignettes Warning in file(con, "w") : cannot open file '/home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-surfaltr/00new/surfaltr/doc/index.html': No such file or directory Error in file(con, "w") : cannot open the connection ERROR: installing vignettes failed * removing ‘/home/biocbuild/bbs-3.14-bioc/R/library/surfaltr’ There are several different solutions suggested in this stackoverflow page (r - Installing package fails when building vignettes ((..)/doc/index.html is missing) - Stack Overflow) . I do have ‘inst/doc’ in my .gitignore file and was wondering if I need to remove it to fix this build issue or is there something else I need to fix? Thank you, Pooja P.S. I have tried sending this email a few times using the email address linked to my package but for some reason the email is not posted to the mailing list and I get a response that says 'The message's content type was not explicitly allowed' [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
