Re: [Bioc-devel] How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE?
Thank you for the info Martin and Michael!
In the particular situation with recount and the xts warning,
re-installing data.table 1.11.8 worked with xts 0.11.2. Details are
further below.
Best,
Leo
On Mon, Nov 5, 2018 at 6:49 PM Michael Lawrence
wrote:
>
> For the general problem of understanding your package dependency structure,
> see http://bioconductor.org/packages/release/bioc/html/pkgDepTools.html.
Thanks for the link!
>
>
> On Mon, Nov 5, 2018 at 3:44 PM Martin Morgan wrote:
>>
>>
>>
>> On 11/5/18, 5:11 PM, "Bioc-devel on behalf of Leonardo Collado Torres"
>> wrote:
>>
>> Hi bioc-devel,
>>
>> recount is getting a warning on Bioc 3.9 (devel) on macOS:
>>
>> * checking whether package ‘recount’ can be installed ... WARNING
>> Found the following significant warnings:
>> Warning: S3 method ‘xts::as.xts.data.table’ was declared in
>> NAMESPACE but not found
>>
>> I'm not sure how to trace this since recount doesn't depend on xts. At
>> least not directly. What is the best way to find which of the recount
>> dependencies is triggering this NAMESPACE warning? While it's a
>> warning in this case, it seems to break the installation of the GitHub
>> package LieberInstitute/recount.bwtool as shown below.
>>
>> Can you reproduce this warning when you load recount in a new session? If
>> so, you can
>>
>> options(warn = 2) # make them errors
>> trace(registerS3methods, tracer = quote(print(package)))
>> library(recount)
Thanks, I didn't know about trace(regiserS3methods, tracer =
quote(print(package))) ! And yes, I can reproduce the problem with
this code.
>>
>>
>> which will print out each package as it is loaded, the last being printed is
>> the culprit.
>>
>> This failed a problem for me, but on the builder I see
>>
>> Tracing registerS3methods(nsInfo$S3methods, package, env) on entry
>> [1] "data.table"
>> Error: package or namespace load failed for ‘recount’:
>> (converted from warning) S3 method ‘xts::as.xts.data.table’ was declared in
>> NAMESPACE but not found
>>
>> The builder has
>>
>> > packageVersion("xts")
>> [1] ‘0.11.1’
>>
>> whereas I have 0.11.2. The reason is because my R installs xts from source
>> where the most recent version is 0.11.2, whereas the builder plays like most
>> mac users and installs built binaries. The last mac binary available is
>> 0.11.1, as summarized here:
>>
>> https://cran.r-project.org/web/packages/xts/index.html
>>
>> where the Published date is 2018-11-05 (today!) and where the binaries are
>> 0.11.1 but source is 0.11.2.
Tracing registerS3methods(nsInfo$S3methods, package, env) on entry
[1] "data.table"
Error: package or namespace load failed for ‘recount’:
(converted from warning) S3 method ‘xts::as.xts.data.table’ was
declared in NAMESPACE but not found
>
> packageVersion('xts')
[1] ‘0.11.2’
>
> sessionInfo()
R Under development (unstable) (2018-11-02 r75540)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.1
Matrix products: default
BLAS:
/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] SummarizedExperiment_1.13.0 DelayedArray_0.9.0
[3] BiocParallel_1.17.0 matrixStats_0.54.0
[5] Biobase_2.43.0 GenomicRanges_1.35.0
[7] GenomeInfoDb_1.19.0 IRanges_2.17.0
[9] S4Vectors_0.21.0BiocGenerics_0.29.1
[11] colorout_1.2-0
loaded via a namespace (and not attached):
[1] bitops_1.0-6 bit64_0.9-7 RColorBrewer_1.1-2
[4] progress_1.2.0 httr_1.3.1 GenomicFiles_1.19.0
[7] tools_3.6.0 backports_1.1.2 R6_2.3.0
[10] rpart_4.1-13 DBI_1.0.0lazyeval_0.2.1
[13] colorspace_1.3-2 nnet_7.3-12 tidyselect_0.2.5
[16] gridExtra_2.3prettyunits_1.0.2bit_1.1-14
[19] compiler_3.6.0 htmlTable_1.12 xml2_1.2.0
[22] rtracklayer_1.43.0 scales_1.0.0 checkmate_1.8.5
[25] readr_1.1.1 stringr_1.3.1digest_0.6.18
[28] Rsamtools_1.35.0 foreign_0.8-71 GEOquery_2.51.0
[31] XVector_0.23.0 base64enc_0.1-3 pkgconfig_2.0.2
[34] htmltools_0.3.6 limma_3.39.1 BSgenome_1.51.0
[37] htmlwidgets_1.3 rlang_0.3.0.1rstudioapi_0.8
[40] RSQLite_2.1.1bindr_0.1.1 acepack_1.4.1
[43] dplyr_0.7.7 VariantAnnotation_1.29.0 RCurl_1.95-4.11
[46] magrittr_1.5 GenomeInfoDbData_1.2.0 Formula_1.2-3
[49] Matrix_1.2-15Rcpp_0.12.19 munsell_0.5.0
[52] stringi_1.2.4zlibbioc_1.29.0
Re: [Bioc-devel] How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE?
For the general problem of understanding your package dependency structure,
see http://bioconductor.org/packages/release/bioc/html/pkgDepTools.html.
On Mon, Nov 5, 2018 at 3:44 PM Martin Morgan
wrote:
>
>
> On 11/5/18, 5:11 PM, "Bioc-devel on behalf of Leonardo Collado Torres" <
> bioc-devel-boun...@r-project.org on behalf of lcoll...@jhu.edu> wrote:
>
> Hi bioc-devel,
>
> recount is getting a warning on Bioc 3.9 (devel) on macOS:
>
> * checking whether package ‘recount’ can be installed ... WARNING
> Found the following significant warnings:
> Warning: S3 method ‘xts::as.xts.data.table’ was declared in
> NAMESPACE but not found
>
> I'm not sure how to trace this since recount doesn't depend on xts. At
> least not directly. What is the best way to find which of the recount
> dependencies is triggering this NAMESPACE warning? While it's a
> warning in this case, it seems to break the installation of the GitHub
> package LieberInstitute/recount.bwtool as shown below.
>
> Can you reproduce this warning when you load recount in a new session? If
> so, you can
>
> options(warn = 2) # make them errors
> trace(registerS3methods, tracer = quote(print(package)))
> library(recount)
>
> which will print out each package as it is loaded, the last being printed
> is the culprit.
>
> This failed a problem for me, but on the builder I see
>
> Tracing registerS3methods(nsInfo$S3methods, package, env) on entry
> [1] "data.table"
> Error: package or namespace load failed for ‘recount’:
> (converted from warning) S3 method ‘xts::as.xts.data.table’ was declared
> in NAMESPACE but not found
>
> The builder has
>
> > packageVersion("xts")
> [1] ‘0.11.1’
>
> whereas I have 0.11.2. The reason is because my R installs xts from source
> where the most recent version is 0.11.2, whereas the builder plays like
> most mac users and installs built binaries. The last mac binary available
> is 0.11.1, as summarized here:
>
> https://cran.r-project.org/web/packages/xts/index.html
>
> where the Published date is 2018-11-05 (today!) and where the binaries are
> 0.11.1 but source is 0.11.2.
>
> A further complexity is that there are NO MAC BINARIES for R-devel so
> basically the build machine is stuck with this situation until the mac
> binaries become available... when binaries become available would be a
> question for the R-sig-mac mailing list, though likely it has been asked /
> answered there before...
>
> Martin
>
> Anyhow, I might just wait a while as was recommended in another thread
> https://stat.ethz.ch/pipermail/bioc-devel/2018-November/014263.html.
> I'm assuming that there are no recount.bwtool R 3.6 macOS users :P
> Though it's worrisome if a package can't depend on recount right now
> on R 3.6 / Bioc 3.9.
>
> Thanks,
> Leo
>
> Main links:
>
> *
> https://bioconductor.org/checkResults/3.9/bioc-LATEST/recount/merida2-checksrc.html
> * https://github.com/leekgroup/recount
> * https://github.com/LieberInstitute/recount.bwtool
>
> Full info:
>
> > library('devtools')
> > install_github('LieberInstitute/recount.bwtool')
> Downloading GitHub repo LieberInstitute/recount.bwtool@master
> Skipping 28 packages ahead of CRAN: AnnotationDbi, Biobase,
> BiocGenerics, BiocParallel, biomaRt, Biostrings, BSgenome,
> DelayedArray, derfinder, derfinderHelper, GenomeInfoDb,
> GenomeInfoDbData, GenomicAlignments, GenomicFeatures, GenomicFiles,
> GenomicRanges, GEOquery, IRanges, limma, qvalue, recount, Rsamtools,
> rtracklayer, S4Vectors, SummarizedExperiment, VariantAnnotation,
> XVector, zlibbioc
> ✔ checking for file
>
> ‘/private/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T/Rtmp8Ho5Vh/remotes85e95180016e/LieberInstitute-recount.bwtool-0de3145/DESCRIPTION’
> (350ms)
> ─ preparing ‘recount.bwtool’:
> ✔ checking DESCRIPTION meta-information ...
> ─ checking for LF line-endings in source and make files and shell
> scripts
> ─ checking for empty or unneeded directories
> ─ building ‘recount.bwtool_0.99.29.tar.gz’
>
> Loading required package: colorout
> * installing *source* package ‘recount.bwtool’ ...
> ** R
> ** inst
> ** byte-compile and prepare package for lazy loading
> Error: package or namespace load failed for ‘recount’:
> (converted from warning) S3 method ‘xts::as.xts.data.table’ was
> declared in NAMESPACE but not found
> Error : package ‘recount’ could not be loaded
> ERROR: lazy loading failed for package ‘recount.bwtool’
> * removing
> ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/recount.bwtool’
> Error in i.p(...) :
> (converted from warning) installation of package
>
> ‘/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmp8Ho5Vh/file85e92ade068f/recount.bwtool_0.99.29.tar.gz’
> had non-zero exit status
> > traceback()
> 20: doWithOneRestart(return(expr), restart)
Re: [Bioc-devel] How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE?
On 11/5/18, 5:11 PM, "Bioc-devel on behalf of Leonardo Collado Torres"
wrote:
Hi bioc-devel,
recount is getting a warning on Bioc 3.9 (devel) on macOS:
* checking whether package ‘recount’ can be installed ... WARNING
Found the following significant warnings:
Warning: S3 method ‘xts::as.xts.data.table’ was declared in
NAMESPACE but not found
I'm not sure how to trace this since recount doesn't depend on xts. At
least not directly. What is the best way to find which of the recount
dependencies is triggering this NAMESPACE warning? While it's a
warning in this case, it seems to break the installation of the GitHub
package LieberInstitute/recount.bwtool as shown below.
Can you reproduce this warning when you load recount in a new session? If so,
you can
options(warn = 2) # make them errors
trace(registerS3methods, tracer = quote(print(package)))
library(recount)
which will print out each package as it is loaded, the last being printed is
the culprit.
This failed a problem for me, but on the builder I see
Tracing registerS3methods(nsInfo$S3methods, package, env) on entry
[1] "data.table"
Error: package or namespace load failed for ‘recount’:
(converted from warning) S3 method ‘xts::as.xts.data.table’ was declared in
NAMESPACE but not found
The builder has
> packageVersion("xts")
[1] ‘0.11.1’
whereas I have 0.11.2. The reason is because my R installs xts from source
where the most recent version is 0.11.2, whereas the builder plays like most
mac users and installs built binaries. The last mac binary available is 0.11.1,
as summarized here:
https://cran.r-project.org/web/packages/xts/index.html
where the Published date is 2018-11-05 (today!) and where the binaries are
0.11.1 but source is 0.11.2.
A further complexity is that there are NO MAC BINARIES for R-devel so basically
the build machine is stuck with this situation until the mac binaries become
available... when binaries become available would be a question for the
R-sig-mac mailing list, though likely it has been asked / answered there
before...
Martin
Anyhow, I might just wait a while as was recommended in another thread
https://stat.ethz.ch/pipermail/bioc-devel/2018-November/014263.html.
I'm assuming that there are no recount.bwtool R 3.6 macOS users :P
Though it's worrisome if a package can't depend on recount right now
on R 3.6 / Bioc 3.9.
Thanks,
Leo
Main links:
*
https://bioconductor.org/checkResults/3.9/bioc-LATEST/recount/merida2-checksrc.html
* https://github.com/leekgroup/recount
* https://github.com/LieberInstitute/recount.bwtool
Full info:
> library('devtools')
> install_github('LieberInstitute/recount.bwtool')
Downloading GitHub repo LieberInstitute/recount.bwtool@master
Skipping 28 packages ahead of CRAN: AnnotationDbi, Biobase,
BiocGenerics, BiocParallel, biomaRt, Biostrings, BSgenome,
DelayedArray, derfinder, derfinderHelper, GenomeInfoDb,
GenomeInfoDbData, GenomicAlignments, GenomicFeatures, GenomicFiles,
GenomicRanges, GEOquery, IRanges, limma, qvalue, recount, Rsamtools,
rtracklayer, S4Vectors, SummarizedExperiment, VariantAnnotation,
XVector, zlibbioc
✔ checking for file
‘/private/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T/Rtmp8Ho5Vh/remotes85e95180016e/LieberInstitute-recount.bwtool-0de3145/DESCRIPTION’
(350ms)
─ preparing ‘recount.bwtool’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘recount.bwtool_0.99.29.tar.gz’
Loading required package: colorout
* installing *source* package ‘recount.bwtool’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘recount’:
(converted from warning) S3 method ‘xts::as.xts.data.table’ was
declared in NAMESPACE but not found
Error : package ‘recount’ could not be loaded
ERROR: lazy loading failed for package ‘recount.bwtool’
* removing
‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/recount.bwtool’
Error in i.p(...) :
(converted from warning) installation of package
‘/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmp8Ho5Vh/file85e92ade068f/recount.bwtool_0.99.29.tar.gz’
had non-zero exit status
> traceback()
20: doWithOneRestart(return(expr), restart)
19: withOneRestart(expr, restarts[[1L]])
18: withRestarts({
.Internal(.signalCondition(simpleWarning(msg, call), msg,
call))
.Internal(.dfltWarn(msg, call))
}, muffleWarning = function() NULL)
17: .signalSimpleWarning("installation of package
‘/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmp8Ho5Vh/file85e92ade068f/recount.bwtool_0.99.29.tar.gz’
[Bioc-devel] How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE?
Hi bioc-devel,
recount is getting a warning on Bioc 3.9 (devel) on macOS:
* checking whether package ‘recount’ can be installed ... WARNING
Found the following significant warnings:
Warning: S3 method ‘xts::as.xts.data.table’ was declared in
NAMESPACE but not found
I'm not sure how to trace this since recount doesn't depend on xts. At
least not directly. What is the best way to find which of the recount
dependencies is triggering this NAMESPACE warning? While it's a
warning in this case, it seems to break the installation of the GitHub
package LieberInstitute/recount.bwtool as shown below.
Anyhow, I might just wait a while as was recommended in another thread
https://stat.ethz.ch/pipermail/bioc-devel/2018-November/014263.html.
I'm assuming that there are no recount.bwtool R 3.6 macOS users :P
Though it's worrisome if a package can't depend on recount right now
on R 3.6 / Bioc 3.9.
Thanks,
Leo
Main links:
*
https://bioconductor.org/checkResults/3.9/bioc-LATEST/recount/merida2-checksrc.html
* https://github.com/leekgroup/recount
* https://github.com/LieberInstitute/recount.bwtool
Full info:
> library('devtools')
> install_github('LieberInstitute/recount.bwtool')
Downloading GitHub repo LieberInstitute/recount.bwtool@master
Skipping 28 packages ahead of CRAN: AnnotationDbi, Biobase,
BiocGenerics, BiocParallel, biomaRt, Biostrings, BSgenome,
DelayedArray, derfinder, derfinderHelper, GenomeInfoDb,
GenomeInfoDbData, GenomicAlignments, GenomicFeatures, GenomicFiles,
GenomicRanges, GEOquery, IRanges, limma, qvalue, recount, Rsamtools,
rtracklayer, S4Vectors, SummarizedExperiment, VariantAnnotation,
XVector, zlibbioc
✔ checking for file
‘/private/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T/Rtmp8Ho5Vh/remotes85e95180016e/LieberInstitute-recount.bwtool-0de3145/DESCRIPTION’
(350ms)
─ preparing ‘recount.bwtool’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘recount.bwtool_0.99.29.tar.gz’
Loading required package: colorout
* installing *source* package ‘recount.bwtool’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘recount’:
(converted from warning) S3 method ‘xts::as.xts.data.table’ was
declared in NAMESPACE but not found
Error : package ‘recount’ could not be loaded
ERROR: lazy loading failed for package ‘recount.bwtool’
* removing
‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/recount.bwtool’
Error in i.p(...) :
(converted from warning) installation of package
‘/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmp8Ho5Vh/file85e92ade068f/recount.bwtool_0.99.29.tar.gz’
had non-zero exit status
> traceback()
20: doWithOneRestart(return(expr), restart)
19: withOneRestart(expr, restarts[[1L]])
18: withRestarts({
.Internal(.signalCondition(simpleWarning(msg, call), msg,
call))
.Internal(.dfltWarn(msg, call))
}, muffleWarning = function() NULL)
17: .signalSimpleWarning("installation of package
‘/var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmp8Ho5Vh/file85e92ade068f/recount.bwtool_0.99.29.tar.gz’
had non-zero exit status",
base::quote(i.p(...)))
16: warning(gettextf("installation of package %s had non-zero exit status",
sQuote(update[i, 1L])), domain = NA)
15: i.p(...)
14: force(code)
13: force(code)
12: with_envvar(c(R_PROFILE_USER = temp_rprofile), {
force(code)
})
11: with_rprofile_user("options(warn = 2)", i.p(...))
10: force(code)
9: with_options(list(warn = 2), with_rprofile_user("options(warn = 2)",
i.p(...)))
8: force(code)
7: with_envvar(c(R_LIBS = lib, R_LIBS_USER = lib, R_LIBS_SITE = lib),
if (should_error_for_warnings()) {
with_options(list(warn = 2), with_rprofile_user("options(warn = 2)",
i.p(...)))
} else {
i.p(...)
})
6: safe_install_packages(pkgdir, repos = NULL, quiet = quiet, type = "source",
...)
5: install(source, dependencies = dependencies, upgrade = upgrade,
force = force, quiet = quiet, build = build, build_opts = build_opts,
repos = repos, type = type, ...)
4: FUN(X[[i]], ...)
3: vapply(remotes, install_remote, ..., FUN.VALUE = character(1))
2: install_remotes(remotes, auth_token = auth_token, host = host,
dependencies = dependencies, upgrade = upgrade, force = force,
quiet = quiet, build = build, build_opts = build_opts, repos = repos,
type = type, ...)
1: install_github("LieberInstitute/recount.bwtool")
> library('recount')
Warning message:
S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE but not found
> options(width = 120)
> sessioninfo::session_info()
─ Session info
───
setting value
version R Under development (unstable) (2018-11-02 r75540)
os macOS Mojave
