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_pgszgb80000gn/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_pgszgb80000gn/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_pgszgb80000gn/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 10.14.1
system x86_64, darwin15.6.0
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2018-11-05
─ Packages
───────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
acepack 1.4.1 2016-10-29 [1] CRAN (R 3.6.0)
AnnotationDbi 1.45.0 2018-10-30 [1] Bioconductor
assertthat 0.2.0 2017-04-11 [1] CRAN (R 3.6.0)
backports 1.1.2 2017-12-13 [1] CRAN (R 3.6.0)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 3.6.0)
bibtex 0.4.2 2017-06-30 [1] CRAN (R 3.6.0)
bindr 0.1.1 2018-03-13 [1] CRAN (R 3.6.0)
bindrcpp 0.2.2 2018-03-29 [1] CRAN (R 3.6.0)
Biobase * 2.43.0 2018-10-30 [1] Bioconductor
BiocGenerics * 0.29.1 2018-11-01 [1] Bioconductor
BiocParallel * 1.17.0 2018-10-30 [1] Bioconductor
biomaRt 2.39.0 2018-10-30 [1] Bioconductor
Biostrings 2.51.0 2018-10-30 [1] Bioconductor
bit 1.1-14 2018-05-29 [1] CRAN (R 3.6.0)
bit64 0.9-7 2017-05-08 [1] CRAN (R 3.6.0)
bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.0)
blob 1.1.1 2018-03-25 [1] CRAN (R 3.6.0)
BSgenome 1.51.0 2018-10-31 [1] Bioconductor
bumphunter 1.25.0 2018-11-05 [1] Github
(rafalab/bumphunter@6569fde)
callr 3.0.0 2018-08-24 [1] CRAN (R 3.6.0)
checkmate 1.8.5 2017-10-24 [1] CRAN (R 3.6.0)
cli 1.0.1 2018-09-25 [1] CRAN (R 3.6.0)
cluster 2.0.7-1 2018-04-13 [1] CRAN (R 3.6.0)
codetools 0.2-15 2016-10-05 [1] CRAN (R 3.6.0)
colorout * 1.2-0 2018-11-02 [1] Github
(jalvesaq/colorout@cc5fbfa)
colorspace 1.3-2 2016-12-14 [1] CRAN (R 3.6.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)
curl 3.2 2018-03-28 [1] CRAN (R 3.6.0)
data.table 1.11.8 2018-09-30 [1] CRAN (R 3.6.0)
DBI 1.0.0 2018-05-02 [1] CRAN (R 3.6.0)
debugme 1.1.0 2017-10-22 [1] CRAN (R 3.6.0)
DelayedArray * 0.9.0 2018-10-30 [1] Bioconductor
derfinder 1.17.0 2018-10-30 [1] Bioconductor
derfinderHelper 1.17.0 2018-10-30 [1] Bioconductor
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.0)
devtools * 2.0.1 2018-10-26 [1] CRAN (R 3.6.0)
digest 0.6.18 2018-10-10 [1] CRAN (R 3.6.0)
doRNG 1.7.1 2018-06-22 [1] CRAN (R 3.6.0)
downloader 0.4 2015-07-09 [1] CRAN (R 3.6.0)
dplyr 0.7.7 2018-10-16 [1] CRAN (R 3.6.0)
foreach 1.4.4 2017-12-12 [1] CRAN (R 3.6.0)
foreign 0.8-71 2018-07-20 [1] CRAN (R 3.6.0)
Formula 1.2-3 2018-05-03 [1] CRAN (R 3.6.0)
fs 1.2.6 2018-08-23 [1] CRAN (R 3.6.0)
GenomeInfoDb * 1.19.0 2018-10-30 [1] Bioconductor
GenomeInfoDbData 1.2.0 2018-11-02 [1] Bioconductor
GenomicAlignments 1.19.0 2018-10-30 [1] Bioconductor
GenomicFeatures 1.35.1 2018-11-02 [1] Bioconductor
GenomicFiles 1.19.0 2018-10-30 [1] Bioconductor
GenomicRanges * 1.35.0 2018-10-30 [1] Bioconductor
GEOquery 2.51.0 2018-10-30 [1] Bioconductor
ggplot2 3.1.0 2018-10-25 [1] CRAN (R 3.6.0)
glue 1.3.0 2018-07-17 [1] CRAN (R 3.6.0)
gridExtra 2.3 2017-09-09 [1] CRAN (R 3.6.0)
gtable 0.2.0 2016-02-26 [1] CRAN (R 3.6.0)
Hmisc 4.1-1 2018-01-03 [1] CRAN (R 3.6.0)
hms 0.4.2 2018-03-10 [1] CRAN (R 3.6.0)
htmlTable 1.12 2018-05-26 [1] CRAN (R 3.6.0)
htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.6.0)
htmlwidgets 1.3 2018-09-30 [1] CRAN (R 3.6.0)
httr 1.3.1 2017-08-20 [1] CRAN (R 3.6.0)
IRanges * 2.17.0 2018-10-30 [1] Bioconductor
iterators 1.0.10 2018-07-13 [1] CRAN (R 3.6.0)
jsonlite 1.5 2017-06-01 [1] CRAN (R 3.6.0)
knitr 1.20 2018-02-20 [1] CRAN (R 3.6.0)
lattice 0.20-38 2018-11-04 [1] CRAN (R 3.6.0)
latticeExtra 0.6-28 2016-02-09 [1] CRAN (R 3.6.0)
lazyeval 0.2.1 2017-10-29 [1] CRAN (R 3.6.0)
limma 3.39.1 2018-11-01 [1] Bioconductor
locfit 1.5-9.1 2013-04-20 [1] CRAN (R 3.6.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0)
Matrix 1.2-15 2018-11-01 [1] CRAN (R 3.6.0)
matrixStats * 0.54.0 2018-07-23 [1] CRAN (R 3.6.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0)
nnet 7.3-12 2016-02-02 [1] CRAN (R 3.6.0)
pillar 1.3.0 2018-07-14 [1] CRAN (R 3.6.0)
pkgbuild 1.0.2 2018-10-16 [1] CRAN (R 3.6.0)
pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.6.0)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.0)
pkgmaker 0.27 2018-05-25 [1] CRAN (R 3.6.0)
plyr 1.8.4 2016-06-08 [1] CRAN (R 3.6.0)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.0)
processx 3.2.0 2018-08-16 [1] CRAN (R 3.6.0)
progress 1.2.0 2018-06-14 [1] CRAN (R 3.6.0)
ps 1.2.0 2018-10-16 [1] CRAN (R 3.6.0)
purrr 0.2.5 2018-05-29 [1] CRAN (R 3.6.0)
qvalue 2.15.0 2018-10-30 [1] Bioconductor
R6 2.3.0 2018-10-04 [1] CRAN (R 3.6.0)
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.6.0)
Rcpp 0.12.19 2018-10-01 [1] CRAN (R 3.6.0)
RCurl 1.95-4.11 2018-07-15 [1] CRAN (R 3.6.0)
readr 1.1.1 2017-05-16 [1] CRAN (R 3.6.0)
recount * 1.9.0 2018-10-30 [1] Bioconductor
registry 0.5 2017-12-03 [1] CRAN (R 3.6.0)
remotes 2.0.2 2018-10-30 [1] CRAN (R 3.6.0)
rentrez 1.2.1 2018-03-05 [1] CRAN (R 3.6.0)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.0)
rlang 0.3.0.1 2018-10-25 [1] CRAN (R 3.6.0)
rngtools 1.3.1 2018-05-15 [1] CRAN (R 3.6.0)
rpart 4.1-13 2018-02-23 [1] CRAN (R 3.6.0)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.0)
Rsamtools 1.35.0 2018-10-30 [1] Bioconductor
RSQLite 2.1.1 2018-05-06 [1] CRAN (R 3.6.0)
rstudioapi 0.8 2018-10-02 [1] CRAN (R 3.6.0)
rtracklayer 1.43.0 2018-10-30 [1] Bioconductor
S4Vectors * 0.21.0 2018-10-30 [1] Bioconductor
scales 1.0.0 2018-08-09 [1] CRAN (R 3.6.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0)
stringi 1.2.4 2018-07-20 [1] CRAN (R 3.6.0)
stringr 1.3.1 2018-05-10 [1] CRAN (R 3.6.0)
SummarizedExperiment * 1.13.0 2018-10-30 [1] Bioconductor
survival 2.43-1 2018-11-03 [1] CRAN (R 3.6.0)
testthat 2.0.1 2018-10-13 [1] CRAN (R 3.6.0)
tibble 1.4.2 2018-01-22 [1] CRAN (R 3.6.0)
tidyr 0.8.2 2018-10-28 [1] CRAN (R 3.6.0)
tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.6.0)
usethis * 1.4.0 2018-08-14 [1] CRAN (R 3.6.0)
VariantAnnotation 1.29.0 2018-10-30 [1] Bioconductor
withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)
XML 3.98-1.16 2018-08-19 [1] CRAN (R 3.6.0)
xml2 1.2.0 2018-01-24 [1] CRAN (R 3.6.0)
xtable 1.8-3 2018-08-29 [1] CRAN (R 3.6.0)
XVector 0.23.0 2018-10-30 [1] Bioconductor
zlibbioc 1.29.0 2018-10-30 [1] Bioconductor
[1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library
>
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