FEDORA-2018-050da4f07f

bugfix update in Fedora 28 for libsbml, libsedml, & 126 more

Status: stable a year ago

Update R to 3.5.0. Rebuild rpy and rkward to match. rpy updated to 2.9.3 in Fedora 28.

All compiled R packages rebuilt (except for R-shogun, because shogun doesn't build right now). Most updated to the latest version.

How to install

sudo dnf upgrade --advisory=FEDORA-2018-050da4f07f

Comments 20

This update has been submitted for testing by spot.

This update has been pushed to testing.

Same problem as the F27 update:

$ mock -r fedora-28-x86_64 --install R-core-3.5.0-1.fc28 --enablerepo=updates-testing R-Rcpp
$ mock -r fedora-28-x86_64 --no-clean --shell
# R
> library(Rcpp)
Error: package or namespace load failed for ‘Rcpp’:
 package ‘Rcpp’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
karma: -1

Bodhi is disabling automatic push to stable due to negative karma. The maintainer may push manually if they determine that the issue is not severe.

Works great! Thanks.

@qulogic: For R-Rcpp, report the issue to the maintainer. This is not directly related to R. R-Rcpp must be rebuilt against R 3.5.0. In the meantime, you should remove R-Rcpp and use the CRAN version via install.packages(Rcpp) instead.

karma: +1

R-Rcpp should be submitted as part of the same update, just like soname bumps.

spot edited this update.

New build(s):

  • R-qtl-1.42.8-1.fc28
  • R-acepack-1.4.1-7.fc28
  • R-affyio-1.50.0-1.fc28
  • R-affy-1.58.0-1.fc28
  • R-ape-5.1-1.fc28
  • R-argon2-0.2.0-2.fc28
  • R-backports-1.1.2-3.fc28
  • R-base64enc-0.1.3-3.fc28
  • R-biglm-0.9.1-13.fc28
  • R-bindrcpp-0.2.2-2.fc28
  • R-Biobase-2.40.0-1.fc28
  • R-BiocParallel-1.14.1-1.fc28
  • R-Biostrings-2.48.0-1.fc28
  • R-bit64-0.9.7-3.fc28
  • R-bitops-1.0.6-9.fc28
  • R-bit-1.1.13-1.fc28
  • R-BufferedMatrix-1.44.0-1.fc28
  • R-BufferedMatrixMethods-1.44.0-1.fc28
  • R-Cairo-1.5.9-4.fc28
  • R-callr-2.0.4-1.fc28
  • R-caTools-1.17.1-8.fc28
  • R-colorspace-1.3.2-2.fc28
  • R-commonmark-1.5-2.fc28
  • R-corpus-0.10.0-2.fc28
  • R-curl-3.2-2.fc28
  • R-date-1.2.38-2.fc28
  • R-deldir-0.1.15-2.fc28
  • R-digest-0.6.15-2.fc28
  • R-expm-0.999.2-6.fc28
  • R-fastmatch-1.1.0-2.fc28
  • R-filehash-2.4.1-3.fc28
  • R-FMStable-0.1.2-2.fc28
  • R-fts-0.9.9-2.fc28
  • R-gamlss.dist-5.0.5-2.fc28
  • R-gdtools-0.1.7-3.fc28
  • R-geepack-1.2.1-3.fc28
  • R-gee-4.13.19-2.fc28
  • R-GenomicAlignments-1.16.0-1.fc28
  • R-GenomicRanges-1.32.3-1.fc28
  • R-getPass-0.2.2-2.fc28
  • R-git2r-0.21.0-2.fc28
  • R-gmp-0.5.13.1-2.fc28
  • R-gss-2.1.9-2.fc28
  • R-gtools-3.5.0-2.fc28
  • R-hexbin-1.27.2-2.fc28
  • R-highlight-0.4.7.2-1.fc28
  • R-htmltools-0.3.6-4.fc28
  • R-httpuv-1.4.3-2.fc28
  • R-IRanges-2.14.10-1.fc28
  • R-jpeg-0.1.8-5.fc28
  • R-jsonlite-1.5-7.fc28
  • R-later-0.7.2-2.fc28
  • R-lazyeval-0.2.1-2.fc28
  • libsbml-5.16.0-8.fc28
  • R-littler-0.3.3-4.fc28
  • R-lmtest-0.9.36-1.fc28
  • R-lubridate-1.7.4-2.fc28
  • R-maanova-1.50.0-1.fc28
  • R-markdown-0.8-5.fc28
  • R-matrixStats-0.53.1-2.fc28
  • R-mime-0.5-3.fc28
  • R-mlbench-2.1.1-2.fc28
  • R-mnormt-1.5.5-2.fc28
  • R-msm-1.6.6-1.fc28
  • R-multtest-2.36.0-1.fc28
  • R-mvtnorm-1.0.7-1.fc28
  • R-openssl-1.0.1-2.fc28
  • R-pbdZMQ-0.3.3-2.fc28
  • R-pdftools-1.7-1.fc28
  • R-plyr-1.8.4-6.fc28
  • R-png-0.1.7-5.fc28
  • R-poLCA-1.4.1-2.fc28
  • R-polyclip-1.8.7-1.fc28
  • R-preprocessCore-1.42.0-1.fc28
  • R-processx-3.1.0-1.fc28
  • R-promises-1.0.1-2.fc28
  • R-Rcompression-0.93.2-20.fc28
  • R-RcppCCTZ-0.2.3-3.fc28
  • R-Rcpp-0.12.16-2.fc28
  • R-RCurl-1.95.4.10-2.fc28
  • R-reshape2-1.4.3-4.fc28
  • R-reticulate-1.7-2.fc28
  • R-rgdal-1.2.20-2.fc28
  • R-rgeos-0.3.26-2.fc28
  • R-RInside-0.2.14-7.fc28
  • R-rlang-0.2.0-2.fc28
  • R-rlecuyer-0.3.4-5.fc28
  • R-Rmpfr-0.7.0-2.fc28
  • R-ROC-1.56.0-1.fc28
  • R-RODBC-1.3.15-5.fc28
  • R-Rsamtools-1.32.0-1.fc28
  • R-Rsolid-0.9.31-24.fc28
  • R-RSQLite-2.1.1-2.fc28
  • R-rtracklayer-1.40.2-1.fc28
  • R-S4Vectors-0.18.2-1.fc28
  • libsedml-0.4.3-10.fc28
  • R-sourcetools-0.1.7-2.fc28
  • R-sp-1.2.7-2.fc28
  • R-statmod-1.4.30-1.fc28
  • R-statnet.common-4.0.0-2.fc28
  • R-stringdist-0.9.4.7-2.fc28
  • R-stringi-1.2.2-1.fc28
  • R-testthat-2.0.0-2.fc28
  • R-tikzDevice-0.11-2.fc28
  • R-tkrplot-0.0.23-2.fc28
  • R-utf8-1.1.3-2.fc28
  • R-uuid-0.1.2-5.fc28
  • R-V8-1.5-5.fc28
  • R-waveslim-1.7.5-8.fc28
  • R-wavethresh-4.6.8-5.fc28
  • R-webp-0.4-2.fc28
  • R-webutils-0.6-2.fc28
  • R-xml2-1.2.0-4.fc28.1
  • R-XML-3.98.1.11-1.fc28
  • R-XVector-0.20.0-1.fc28
  • R-yaml-2.1.19-2.fc28
  • R-zoo-1.8.1-1.fc28
  • R-DBI-1.0.0-1.fc28
  • R-plogr-0.2.0-1.fc28
  • R-prettyunits-1.0.2-1.fc28
  • R-blob-1.1.1-2.fc28
  • R-BiocGenerics-0.26.0-1.fc28
  • R-GenomeInfoDb-1.16.0-1.fc28
  • R-SummarizedExperiment-1.10.1-1.fc28
  • v8-314-3.14.5.10-10.fc28

Karma has been reset.

This update has been submitted for testing by spot.

This update has been pushed to testing.

Works great!

karma: +1

Thank you! Looks good to me.

karma: +1

Works great! LGTM! =)

karma: +1

This update has reached the stable karma threshold and can be pushed to stable now if the maintainer wishes.

I ran:

$ mock -r fedora-28-x86_64 --dnf-cmd -- install 'R-*' --skip-broken
$ mock -r fedora-28-x86_64 --dnf-cmd list 'R-*' | awk '{print $1}' | sed -e 's/\.[^.]\+$//g' -e 's/^R-//' -e 's/-devel$//' | sort -u > pkgs
$ mock -r fedora-28-x86_64 --copyin pkgs /
$ mock -r fedora-28-x86_64 --shell
# for p in `cat pkgs`; do echo "library($p); quit()" | R --quiet --vanilla; done &> results
$ mock -r fedora-28-x86_64 --copyout /results results-f28

then did it again with --enablerepo=updates-testing, and diffed the results.

With this update, we are now able to also install:

  • R-blob,
  • R-orcutt, and
  • R-prettyunits.

Also, now able to correctly load:

  • R-affy,
  • R-affydata,
  • R-lmtest,
  • R-maanova,
  • R-msm,
  • R-multcomp,
  • R-mvtnorm,
  • R-preprocessCore,
  • R-RM2,
  • R-sandwich,
  • R-statmod,
  • R-systemfit, and
  • R-waveslim.

But now these packages are broken:

  • R-chron,
  • R-COPASI,
  • R-GeneR,
  • R-quadprog,
  • R-reshape, and
  • R-roxygen2.

I have rebuilt R-chron, R-quadprog, R-reshape, and R-roxygen2, but I don't have permissions to build the other two. If you don't want to wait another week, I can submit these as a separate update.

karma: -1

Ugh, I added +1s on a bunch of the FTBFS bugs, but bodhi didn't save it.

qulogic, thanks for the follow-up. Let's go ahead and let this update land, and do the others as a separate update.

R-COPASI did get rebuilt, but the maintainer put it into an update of its own (then, deleted it).

This update has been submitted for batched by spot.

This update has been submitted for batched by spot.

This update has been submitted for stable by spot.

This update has been pushed to stable.

Content Type
RPM
Status
stable
Test Gating
Submitted by
Update Type
bugfix
Update Severity
unspecified
Karma
+2
stable threshold: 3
unstable threshold: -3
Autopush
Disabled
Dates
submitted a year ago
in testing a year ago
in stable a year ago
modified a year ago

Related Bugs 28

00 #1405667 R-zoo-1.8-1 is available
00 #1555498 R-Biostrings: FTBFS in F28
00 #1555515 R-ROC: FTBFS in F28
00 #1555516 R-RODBC: FTBFS in F28
00 #1555521 R-Rsolid: FTBFS in F28
00 #1555525 R-XML: FTBFS in F28
00 #1555528 R-affy: FTBFS in F28
00 #1555530 R-affyio: FTBFS in F28
00 #1555532 R-bitops: FTBFS in F28
00 #1555533 R-caTools: FTBFS in F28
00 #1555547 R-maanova: FTBFS in F28
00 #1555552 R-msm: FTBFS in F28
00 #1555555 R-multtest: FTBFS in F28
00 #1555556 R-mvtnorm: FTBFS in F28
00 #1555561 R-preprocessCore: FTBFS in F28
00 #1555564 R-rlecuyer: FTBFS in F28
00 #1555569 R-statmod: FTBFS in F28
00 #1555574 R-waveslim: FTBFS in F28
00 #1555575 R-wavethresh: FTBFS in F28
00 #1556527 v8-314: FTBFS in F28
00 #1560254 R-curl-3.2 is available
00 #1563656 R-lmtest-0.9-36 is available
00 #1567573 rpy-2.9.3 is available
00 #1570804 R-3.5.0 is available
00 #1574116 R-stringi-1.2.2 is available
00 #1575172 R-httpuv-1.4.3 is available
00 #1578961 Review Request: R-prettyunits - Pretty, Human Readable Formatting of Quantities
00 #1578963 Review Request: R-blob - A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS')
libsbml-5.16.0-8.fc28
libsedml-0.4.3-10.fc28
R-3.5.0-1.fc28
R-acepack-1.4.1-7.fc28
R-affy-1.58.0-1.fc28
R-affyio-1.50.0-1.fc28
R-ape-5.1-1.fc28
R-argon2-0.2.0-2.fc28
R-backports-1.1.2-3.fc28
R-base64enc-0.1.3-3.fc28
R-biglm-0.9.1-13.fc28
R-bindrcpp-0.2.2-2.fc28
R-Biobase-2.40.0-1.fc28
R-BiocGenerics-0.26.0-1.fc28
R-BiocParallel-1.14.1-1.fc28
R-Biostrings-2.48.0-1.fc28
R-bit-1.1.13-1.fc28
R-bit64-0.9.7-3.fc28
R-bitops-1.0.6-9.fc28
R-blob-1.1.1-2.fc28
R-BufferedMatrix-1.44.0-1.fc28
R-BufferedMatrixMethods-1.44.0-1.fc28
R-Cairo-1.5.9-4.fc28
R-callr-2.0.4-1.fc28
R-caTools-1.17.1-8.fc28
R-colorspace-1.3.2-2.fc28
R-commonmark-1.5-2.fc28
R-corpus-0.10.0-2.fc28
R-curl-3.2-2.fc28
R-date-1.2.38-2.fc28
R-DBI-1.0.0-1.fc28
R-deldir-0.1.15-2.fc28
R-digest-0.6.15-2.fc28
R-expm-0.999.2-6.fc28
R-fastmatch-1.1.0-2.fc28
R-filehash-2.4.1-3.fc28
R-FMStable-0.1.2-2.fc28
R-fts-0.9.9-2.fc28
R-gamlss.dist-5.0.5-2.fc28
R-gdtools-0.1.7-3.fc28
R-gee-4.13.19-2.fc28
R-geepack-1.2.1-3.fc28
R-GenomeInfoDb-1.16.0-1.fc28
R-GenomicAlignments-1.16.0-1.fc28
R-GenomicRanges-1.32.3-1.fc28
R-getPass-0.2.2-2.fc28
R-git2r-0.21.0-2.fc28
R-gmp-0.5.13.1-2.fc28
R-gss-2.1.9-2.fc28
R-gtools-3.5.0-2.fc28
R-hexbin-1.27.2-2.fc28
R-highlight-0.4.7.2-1.fc28
R-htmltools-0.3.6-4.fc28
R-httpuv-1.4.3-2.fc28
R-IRanges-2.14.10-1.fc28
R-jpeg-0.1.8-5.fc28
R-jsonlite-1.5-7.fc28
rkward-0.6.5-15.fc28
R-later-0.7.2-2.fc28
R-lazyeval-0.2.1-2.fc28
R-littler-0.3.3-4.fc28
R-lmtest-0.9.36-1.fc28
R-lubridate-1.7.4-2.fc28
R-maanova-1.50.0-1.fc28
R-markdown-0.8-5.fc28
R-matrixStats-0.53.1-2.fc28
R-mime-0.5-3.fc28
R-mlbench-2.1.1-2.fc28
R-mnormt-1.5.5-2.fc28
R-msm-1.6.6-1.fc28
R-multtest-2.36.0-1.fc28
R-mvtnorm-1.0.7-1.fc28
R-openssl-1.0.1-2.fc28
R-pbdZMQ-0.3.3-2.fc28
R-pdftools-1.7-1.fc28
R-plogr-0.2.0-1.fc28
R-plyr-1.8.4-6.fc28
R-png-0.1.7-5.fc28
R-poLCA-1.4.1-2.fc28
R-polyclip-1.8.7-1.fc28
R-preprocessCore-1.42.0-1.fc28
R-prettyunits-1.0.2-1.fc28
R-processx-3.1.0-1.fc28
R-promises-1.0.1-2.fc28
rpy-2.9.3-1.fc28
R-qtl-1.42.8-1.fc28
R-Rcompression-0.93.2-20.fc28
R-Rcpp-0.12.16-2.fc28
R-RcppCCTZ-0.2.3-3.fc28
R-RCurl-1.95.4.10-2.fc28
R-reshape2-1.4.3-4.fc28
R-reticulate-1.7-2.fc28
R-rgdal-1.2.20-2.fc28
R-rgeos-0.3.26-2.fc28
R-RInside-0.2.14-7.fc28
R-rlang-0.2.0-2.fc28
R-rlecuyer-0.3.4-5.fc28
R-Rmpfr-0.7.0-2.fc28
R-ROC-1.56.0-1.fc28
R-RODBC-1.3.15-5.fc28
R-Rsamtools-1.32.0-1.fc28
R-Rsolid-0.9.31-24.fc28
R-RSQLite-2.1.1-2.fc28
R-rtracklayer-1.40.2-1.fc28
R-S4Vectors-0.18.2-1.fc28
R-sourcetools-0.1.7-2.fc28
R-sp-1.2.7-2.fc28
R-statmod-1.4.30-1.fc28
R-statnet.common-4.0.0-2.fc28
R-stringdist-0.9.4.7-2.fc28
R-stringi-1.2.2-1.fc28
R-SummarizedExperiment-1.10.1-1.fc28
R-testthat-2.0.0-2.fc28
R-tikzDevice-0.11-2.fc28
R-tkrplot-0.0.23-2.fc28
R-utf8-1.1.3-2.fc28
R-uuid-0.1.2-5.fc28
R-V8-1.5-5.fc28
R-waveslim-1.7.5-8.fc28
R-wavethresh-4.6.8-5.fc28
R-webp-0.4-2.fc28
R-webutils-0.6-2.fc28
R-xml2-1.2.0-4.fc28.1
R-XML-3.98.1.11-1.fc28
R-XVector-0.20.0-1.fc28
R-yaml-2.1.19-2.fc28
R-zoo-1.8.1-1.fc28
v8-314-3.14.5.10-10.fc28

Automated Test Results