FEDORA-2018-b11015006b

bugfix update in Fedora 27 for libsbml, libsedml, & 119 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. Rebuild all compiled R modules, except R-shogun (shogun does not build right now).

Comments 18

This update has been submitted for testing by spot.

This update has been pushed to testing.

Much like a minor Python version bump, this appears to require rebuilding all R packages. For example,

$ mock -r fedora-27-x86_64 --install R-core-3.5.0-1.fc27 --enablerepo=updates-testing R-Rcpp
$ mock -r fedora-27-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

Not sure why negative karma did not get posted before.

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.

spot edited this update.

New build(s):

  • R-blob-1.1.1-2.fc27
  • R-prettyunits-1.0.2-1.fc27
  • R-zoo-1.8.1-1.fc27
  • R-yaml-2.1.19-2.fc27
  • R-XVector-0.16.0-4.fc27
  • R-XML-3.98.1.7-4.fc27
  • R-xml2-1.2.0-4.fc27
  • R-webutils-0.6-2.fc27
  • R-webp-0.4-2.fc27
  • R-wavethresh-4.6.8-5.fc27
  • R-waveslim-1.7.5-8.fc27
  • R-V8-1.5-5.fc27
  • R-uuid-0.1.2-5.fc27
  • R-utf8-1.1.3-2.fc27
  • R-tkrplot-0.0.23-2.fc27
  • R-tikzDevice-0.11-2.fc27
  • R-testthat-1.0.2-6.fc27
  • R-stringi-1.2.2-1.fc27
  • R-stringdist-0.9.4.7-2.fc27
  • R-statnet.common-4.0.0-2.fc27
  • R-statmod-1.4.30-1.fc27
  • R-sp-1.2.7-2.fc27
  • R-sourcetools-0.1.7-2.fc27
  • libsedml-0.4.3-10.fc27
  • R-S4Vectors-0.14.3-4.fc27
  • R-rtracklayer-1.36.3-4.fc27
  • R-RSQLite-1.1.2-5.fc27
  • R-Rsolid-0.9.31-24.fc27
  • R-Rsamtools-1.28.0-4.fc27
  • R-RODBC-1.3.15-5.fc27
  • R-ROC-1.46.0-6.fc27
  • R-Rmpfr-0.7.0-2.fc27
  • R-rlecuyer-0.3.4-5.fc27
  • R-rlang-0.2.0-2.fc27
  • R-RInside-0.2.14-7.fc27
  • R-rgeos-0.3.26-2.fc27
  • R-rgdal-1.2.20-2.fc27
  • R-reticulate-1.7-2.fc27
  • R-reshape2-1.4.3-4.fc27
  • R-RCurl-1.95.4.8-4.fc27
  • R-Rcpp-0.12.16-2.fc27
  • R-RcppCCTZ-0.2.3-3.fc27
  • R-Rcompression-0.93.2-20.fc27
  • R-qtl-1.42.8-1.fc27
  • R-processx-2.0.0.1-2.fc27
  • R-preprocessCore-1.38.1-4.fc27
  • R-polyclip-1.8.7-1.fc27
  • R-poLCA-1.4.1-2.fc27
  • R-png-0.1.7-5.fc27
  • R-plyr-1.8.4-6.fc27
  • R-pdftools-1.7-1.fc27
  • R-pbdZMQ-0.3.3-2.fc27
  • R-openssl-1.0.1-2.fc27
  • R-mvtnorm-1.0.7-1.fc27
  • R-multtest-2.36.0-1.fc27
  • R-msm-1.6.4-4.fc27
  • R-mnormt-1.5.5-2.fc27
  • R-mlbench-2.1.1-2.fc27
  • R-mime-0.5-3.fc27
  • R-matrixStats-0.52.2-4.fc27
  • R-markdown-0.8-5.fc27
  • R-maanova-1.46.1-4.fc27
  • R-lubridate-1.7.3-5.fc27
  • R-lmtest-0.9.36-1.fc27
  • R-littler-0.3.3-4.fc27
  • libsbml-5.16.0-8.fc27
  • R-lazyeval-0.2.1-2.fc27
  • R-later-0.7.2-2.fc27
  • R-jsonlite-1.5-7.fc27
  • R-jpeg-0.1.8-5.fc27
  • R-IRanges-2.10.1-4.fc27
  • R-httpuv-1.3.6.2-3.fc27
  • R-htmltools-0.3.6-4.fc27
  • R-highlight-0.4.7.2-1.fc27
  • R-hexbin-1.27.2-2.fc27
  • R-gtools-3.5.0-2.fc27
  • R-gss-2.1.9-2.fc27
  • R-gmp-0.5.13.1-2.fc27
  • R-git2r-0.21.0-2.fc27
  • R-getPass-0.2.2-2.fc27
  • R-GenomicRanges-1.28.3-4.fc27
  • R-GenomicAlignments-1.12.1-4.fc27
  • R-gee-4.13.19-2.fc27
  • R-geepack-1.2.1-3.fc27
  • R-gdtools-0.1.7-3.fc27
  • R-gamlss.dist-5.0.5-2.fc27
  • R-fts-0.9.9-2.fc27
  • R-FMStable-0.1.2-2.fc27
  • R-filehash-2.4.1-3.fc27
  • R-fastmatch-1.1.0-2.fc27
  • R-expm-0.999.2-6.fc27
  • R-digest-0.6.12-4.fc27
  • R-deldir-0.1.15-2.fc27
  • R-date-1.2.38-2.fc27
  • R-curl-3.2-2.fc27
  • R-corpus-0.10.0-2.fc27
  • R-commonmark-1.5-2.fc27
  • R-colorspace-1.3.2-2.fc27
  • R-caTools-1.17.1-8.fc27
  • R-callr-2.0.3-2.fc27
  • R-Cairo-1.5.9-4.fc27
  • R-BufferedMatrixMethods-1.44.0-1.fc27
  • R-BufferedMatrix-1.44.0-1.fc27
  • R-bit64-0.9.7-3.fc27
  • R-bitops-1.0.6-9.fc27
  • R-bit-1.1.13-1.fc27
  • R-Biostrings-2.44.0-4.fc27
  • R-BiocParallel-1.10.1-3.fc27
  • R-Biobase-2.36.2-4.fc27
  • R-bindrcpp-0.2.2-2.fc27
  • R-biglm-0.9.1-13.fc27
  • R-base64enc-0.1.3-3.fc27
  • R-backports-1.1.2-3.fc27
  • R-argon2-0.2.0-2.fc27
  • R-ape-5.1-1.fc27
  • R-affy-1.54.0-4.fc27
  • R-affyio-1.46.0-4.fc27
  • R-acepack-1.4.1-7.fc27

Karma has been reset.

This update has been submitted for testing by spot.

This update has obsoleted R-polyclip-1.8.4-1.fc27, and has inherited its bugs and notes.

spot edited this update.

New build(s):

  • R-blob-1.1.1-2.fc27
  • R-prettyunits-1.0.2-1.fc27
  • R-zoo-1.8.1-1.fc27
  • R-yaml-2.1.19-2.fc27
  • R-XVector-0.16.0-4.fc27
  • R-XML-3.98.1.7-4.fc27
  • R-xml2-1.2.0-4.fc27
  • R-webutils-0.6-2.fc27
  • R-webp-0.4-2.fc27
  • R-wavethresh-4.6.8-5.fc27
  • R-waveslim-1.7.5-8.fc27
  • R-V8-1.5-5.fc27
  • R-uuid-0.1.2-5.fc27
  • R-utf8-1.1.3-2.fc27
  • R-tkrplot-0.0.23-2.fc27
  • R-tikzDevice-0.11-2.fc27
  • R-testthat-1.0.2-6.fc27
  • R-stringi-1.2.2-1.fc27
  • R-stringdist-0.9.4.7-2.fc27
  • R-statnet.common-4.0.0-2.fc27
  • R-statmod-1.4.30-1.fc27
  • R-sp-1.2.7-2.fc27
  • R-sourcetools-0.1.7-2.fc27
  • libsedml-0.4.3-10.fc27
  • R-S4Vectors-0.14.3-4.fc27
  • R-rtracklayer-1.36.3-4.fc27
  • R-RSQLite-1.1.2-5.fc27
  • R-Rsolid-0.9.31-24.fc27
  • R-Rsamtools-1.28.0-4.fc27
  • R-RODBC-1.3.15-5.fc27
  • R-ROC-1.46.0-6.fc27
  • R-Rmpfr-0.7.0-2.fc27
  • R-rlecuyer-0.3.4-5.fc27
  • R-rlang-0.2.0-2.fc27
  • R-RInside-0.2.14-7.fc27
  • R-rgeos-0.3.26-2.fc27
  • R-rgdal-1.2.20-2.fc27
  • R-reticulate-1.7-2.fc27
  • R-reshape2-1.4.3-4.fc27
  • R-RCurl-1.95.4.8-4.fc27
  • R-Rcpp-0.12.16-2.fc27
  • R-RcppCCTZ-0.2.3-3.fc27
  • R-Rcompression-0.93.2-20.fc27
  • R-qtl-1.42.8-1.fc27
  • R-processx-2.0.0.1-2.fc27
  • R-preprocessCore-1.38.1-4.fc27
  • R-polyclip-1.8.7-1.fc27
  • R-poLCA-1.4.1-2.fc27
  • R-png-0.1.7-5.fc27
  • R-plyr-1.8.4-6.fc27
  • R-pdftools-1.7-1.fc27
  • R-pbdZMQ-0.3.3-2.fc27
  • R-openssl-1.0.1-2.fc27
  • R-mvtnorm-1.0.7-1.fc27
  • R-multtest-2.36.0-1.fc27
  • R-msm-1.6.4-4.fc27
  • R-mnormt-1.5.5-2.fc27
  • R-mlbench-2.1.1-2.fc27
  • R-mime-0.5-3.fc27
  • R-matrixStats-0.52.2-4.fc27
  • R-markdown-0.8-5.fc27
  • R-maanova-1.46.1-4.fc27
  • R-lubridate-1.7.3-5.fc27
  • R-lmtest-0.9.36-1.fc27
  • R-littler-0.3.3-4.fc27
  • libsbml-5.16.0-8.fc27
  • R-lazyeval-0.2.1-2.fc27
  • R-later-0.7.2-2.fc27
  • R-jsonlite-1.5-7.fc27
  • R-jpeg-0.1.8-5.fc27
  • R-IRanges-2.10.1-4.fc27
  • R-httpuv-1.3.6.2-3.fc27
  • R-htmltools-0.3.6-4.fc27
  • R-highlight-0.4.7.2-1.fc27
  • R-hexbin-1.27.2-2.fc27
  • R-gtools-3.5.0-2.fc27
  • R-gss-2.1.9-2.fc27
  • R-gmp-0.5.13.1-2.fc27
  • R-git2r-0.21.0-2.fc27
  • R-getPass-0.2.2-2.fc27
  • R-GenomicRanges-1.28.3-4.fc27
  • R-GenomicAlignments-1.12.1-4.fc27
  • R-gee-4.13.19-2.fc27
  • R-geepack-1.2.1-3.fc27
  • R-gdtools-0.1.7-3.fc27
  • R-gamlss.dist-5.0.5-2.fc27
  • R-fts-0.9.9-2.fc27
  • R-FMStable-0.1.2-2.fc27
  • R-filehash-2.4.1-3.fc27
  • R-fastmatch-1.1.0-2.fc27
  • R-expm-0.999.2-6.fc27
  • R-digest-0.6.12-4.fc27
  • R-deldir-0.1.15-2.fc27
  • R-date-1.2.38-2.fc27
  • R-curl-3.2-2.fc27
  • R-corpus-0.10.0-2.fc27
  • R-commonmark-1.5-2.fc27
  • R-colorspace-1.3.2-2.fc27
  • R-caTools-1.17.1-8.fc27
  • R-callr-2.0.3-2.fc27
  • R-Cairo-1.5.9-4.fc27
  • R-BufferedMatrixMethods-1.44.0-1.fc27
  • R-BufferedMatrix-1.44.0-1.fc27
  • R-bit64-0.9.7-3.fc27
  • R-bitops-1.0.6-9.fc27
  • R-bit-1.1.13-1.fc27
  • R-Biostrings-2.44.0-4.fc27
  • R-BiocParallel-1.10.1-3.fc27
  • R-Biobase-2.36.2-4.fc27
  • R-bindrcpp-0.2.2-2.fc27
  • R-biglm-0.9.1-13.fc27
  • R-base64enc-0.1.3-3.fc27
  • R-backports-1.1.2-3.fc27
  • R-argon2-0.2.0-2.fc27
  • R-ape-5.1-1.fc27
  • R-affy-1.54.0-4.fc27
  • R-affyio-1.46.0-4.fc27
  • R-acepack-1.4.1-7.fc27

Karma has been reset.

This update has been submitted for testing by spot.

This update has been pushed to testing.

This update has reached 7 days in testing and can be pushed to stable now if the maintainer wishes

I ran:

$ mock -r fedora-27-x86_64 --dnf-cmd -- install 'R-*' --skip-broken
$ mock -r fedora-27-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-27-x86_64 --copyin pkgs /
$ mock -r fedora-27-x86_64 --shell
# for p in `cat pkgs`; do echo "library($p); quit()" | R --quiet --vanilla; done &> results
$ mock -r fedora-27-x86_64 --copyout /results results-f27

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

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

  • R-blob, and
  • R-prettyunits.

Also, now able to correctly load:

  • R-future,
  • R-listenv,
  • R-promises,
  • R-R.cache, and
  • R-R.rsp.

But now these packages are broken:

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

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

Those 4 rebuilds have spent their week in testing; is this update going to get pushed to stable?

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.

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Content Type
RPM
Status
stable
Test Gating
Submitted by
Update Type
bugfix
Update Severity
unspecified
Karma
-1
stable threshold: 3
unstable threshold: -3
Autopush (karma)
Disabled
Autopush (time)
Disabled
Dates
submitted a year ago
in testing a year ago
in stable a year ago
modified a year ago

Related Bugs 2

00 #1567573 rpy-2.9.3 is available
00 #1570804 R-3.5.0 is available
libsbml-5.16.0-8.fc27
libsedml-0.4.3-10.fc27
R-3.5.0-1.fc27
R-acepack-1.4.1-7.fc27
R-affy-1.54.0-4.fc27
R-affyio-1.46.0-4.fc27
R-ape-5.1-1.fc27
R-argon2-0.2.0-2.fc27
R-backports-1.1.2-3.fc27
R-base64enc-0.1.3-3.fc27
R-biglm-0.9.1-13.fc27
R-bindrcpp-0.2.2-2.fc27
R-Biobase-2.36.2-4.fc27
R-BiocParallel-1.10.1-3.fc27
R-Biostrings-2.44.0-4.fc27
R-bit-1.1.13-1.fc27
R-bit64-0.9.7-3.fc27
R-bitops-1.0.6-9.fc27
R-blob-1.1.1-2.fc27
R-BufferedMatrix-1.44.0-1.fc27
R-BufferedMatrixMethods-1.44.0-1.fc27
R-Cairo-1.5.9-4.fc27
R-callr-2.0.3-2.fc27
R-caTools-1.17.1-8.fc27
R-colorspace-1.3.2-2.fc27
R-commonmark-1.5-2.fc27
R-corpus-0.10.0-2.fc27
R-curl-3.2-2.fc27
R-date-1.2.38-2.fc27
R-deldir-0.1.15-2.fc27
R-digest-0.6.12-4.fc27
R-expm-0.999.2-6.fc27
R-fastmatch-1.1.0-2.fc27
R-filehash-2.4.1-3.fc27
R-FMStable-0.1.2-2.fc27
R-fts-0.9.9-2.fc27
R-gamlss.dist-5.0.5-2.fc27
R-gdtools-0.1.7-3.fc27
R-gee-4.13.19-2.fc27
R-geepack-1.2.1-3.fc27
R-GenomicAlignments-1.12.1-4.fc27
R-GenomicRanges-1.28.3-4.fc27
R-getPass-0.2.2-2.fc27
R-git2r-0.21.0-2.fc27
R-gmp-0.5.13.1-2.fc27
R-gss-2.1.9-2.fc27
R-gtools-3.5.0-2.fc27
R-hexbin-1.27.2-2.fc27
R-highlight-0.4.7.2-1.fc27
R-htmltools-0.3.6-4.fc27
R-httpuv-1.3.6.2-3.fc27
R-IRanges-2.10.1-4.fc27
R-jpeg-0.1.8-5.fc27
R-jsonlite-1.5-7.fc27
rkward-0.6.5-15.fc27
R-later-0.7.2-2.fc27
R-lazyeval-0.2.1-2.fc27
R-littler-0.3.3-4.fc27
R-lmtest-0.9.36-1.fc27
R-lubridate-1.7.3-5.fc27
R-maanova-1.46.1-4.fc27
R-markdown-0.8-5.fc27
R-matrixStats-0.52.2-4.fc27
R-mime-0.5-3.fc27
R-mlbench-2.1.1-2.fc27
R-mnormt-1.5.5-2.fc27
R-msm-1.6.4-4.fc27
R-multtest-2.36.0-1.fc27
R-mvtnorm-1.0.7-1.fc27
R-openssl-1.0.1-2.fc27
R-pbdZMQ-0.3.3-2.fc27
R-pdftools-1.7-1.fc27
R-plyr-1.8.4-6.fc27
R-png-0.1.7-5.fc27
R-poLCA-1.4.1-2.fc27
R-polyclip-1.8.7-1.fc27
R-preprocessCore-1.38.1-4.fc27
R-prettyunits-1.0.2-1.fc27
R-processx-2.0.0.1-2.fc27
rpy-2.8.6-7.fc27
R-qtl-1.42.8-1.fc27
R-Rcompression-0.93.2-20.fc27
R-Rcpp-0.12.16-2.fc27
R-RcppCCTZ-0.2.3-3.fc27
R-RCurl-1.95.4.8-4.fc27
R-reshape2-1.4.3-4.fc27
R-reticulate-1.7-2.fc27
R-rgdal-1.2.20-2.fc27
R-rgeos-0.3.26-2.fc27
R-RInside-0.2.14-7.fc27
R-rlang-0.2.0-2.fc27
R-rlecuyer-0.3.4-5.fc27
R-Rmpfr-0.7.0-2.fc27
R-ROC-1.46.0-6.fc27
R-RODBC-1.3.15-5.fc27
R-Rsamtools-1.28.0-4.fc27
R-Rsolid-0.9.31-24.fc27
R-RSQLite-1.1.2-5.fc27
R-rtracklayer-1.36.3-4.fc27
R-S4Vectors-0.14.3-4.fc27
R-sourcetools-0.1.7-2.fc27
R-sp-1.2.7-2.fc27
R-statmod-1.4.30-1.fc27
R-statnet.common-4.0.0-2.fc27
R-stringdist-0.9.4.7-2.fc27
R-stringi-1.2.2-1.fc27
R-testthat-1.0.2-6.fc27
R-tikzDevice-0.11-2.fc27
R-tkrplot-0.0.23-2.fc27
R-utf8-1.1.3-2.fc27
R-uuid-0.1.2-5.fc27
R-V8-1.5-5.fc27
R-waveslim-1.7.5-8.fc27
R-wavethresh-4.6.8-5.fc27
R-webp-0.4-2.fc27
R-webutils-0.6-2.fc27
R-xml2-1.2.0-4.fc27
R-XML-3.98.1.7-4.fc27
R-XVector-0.16.0-4.fc27
R-yaml-2.1.19-2.fc27
R-zoo-1.8.1-1.fc27

Automated Test Results