[MacPorts] #67521: Sometimes R fails to update dependencies when a package is installed, which may break the build, if such an update is required

MacPorts noreply at macports.org
Sun May 28 12:23:14 UTC 2023 

#67521: Sometimes R fails to update dependencies when a package is installed, which
may break the build, if such an update is required
--------------------------+----------------------
 Reporter:  barracuda156  |      Owner:  (none)
     Type:  defect        |     Status:  assigned
 Priority:  Normal        |  Milestone:
Component:  ports         |    Version:  2.8.1
 Keywords:                |       Port:  R
--------------------------+----------------------
 I do not know why this happens, but it seems pretty random and does not
 depend on a specific system (i.e. occurs on all of my test systems).
 Happened quite a number of times, here is an example.

 R-BiocStyle explicitly depends on R-bookdown:
 https://ports.macports.org/port/R-BiocStyle/details

 Here I am installing R-BiocStyle, which is asked for by a port depending
 on it:
 {{{
 * building ‘BiocStyle_2.28.0.tar.gz’

 --->  Building R-BiocStyle
 --->  Staging R-BiocStyle into destroot
 . changed
         gid expected 0 found 80 modified
 ./usr missing (created)
 . missing (directory not created: File exists)
 ./Applications missing (created)
 ./Developer missing (created)
 ./Library missing (created)
 . changed
         gid expected 80 found 0 modified
 ./bin missing (created)
 ./etc missing (created)
 ./include missing (created)
 ./lib missing (created)
 ./lib/pkgconfig missing (created)
 ./libexec missing (created)
 ./sbin missing (created)
 ./share missing (created)
 ./share/doc missing (created)
 ./share/info missing (created)
 ./share/man missing (created)
 ./share/man/cat1 missing (created)
 ./share/man/cat2 missing (created)
 ./share/man/cat3 missing (created)
 ./share/man/cat4 missing (created)
 ./share/man/cat5 missing (created)
 ./share/man/cat6 missing (created)
 ./share/man/cat7 missing (created)
 ./share/man/cat8 missing (created)
 ./share/man/cat9 missing (created)
 ./share/man/catl missing (created)
 ./share/man/catn missing (created)
 ./share/man/man1 missing (created)
 ./share/man/man2 missing (created)
 ./share/man/man3 missing (created)
 ./share/man/man4 missing (created)
 ./share/man/man5 missing (created)
 ./share/man/man6 missing (created)
 ./share/man/man7 missing (created)
 ./share/man/man8 missing (created)
 ./share/man/man9 missing (created)
 ./share/man/manl missing (created)
 ./share/man/mann missing (created)
 ./share/nls missing (created)
 ./share/nls/C missing (created)
 ./share/nls/af_ZA.ISO8859-1 missing (created)
 ./share/nls/af_ZA.ISO8859-15 missing (created)
 ./share/nls/bg_BG.CP1251 missing (created)
 ./share/nls/cs_CZ.ISO8859-2 missing (created)
 ./share/nls/da_DK.ISO8859-1 missing (created)
 ./share/nls/da_DK.ISO8859-15 missing (created)
 ./share/nls/de_AT.ISO8859-1 missing (created)
 ./share/nls/de_AT.ISO8859-15 missing (created)
 ./share/nls/de_CH.ISO8859-1 missing (created)
 ./share/nls/de_CH.ISO8859-15 missing (created)
 ./share/nls/de_DE.ISO8859-1 missing (created)
 ./share/nls/de_DE.ISO8859-15 missing (created)
 ./share/nls/el_GR.ISO8859-7 missing (created)
 ./share/nls/en_AU.ISO8859-1 missing (created)
 ./share/nls/en_AU.ISO8859-15 missing (created)
 ./share/nls/en_AU.US-ASCII missing (created)
 ./share/nls/en_CA.ISO8859-1 missing (created)
 ./share/nls/en_CA.ISO8859-15 missing (created)
 ./share/nls/en_CA.US-ASCII missing (created)
 ./share/nls/en_GB.ISO8859-1 missing (created)
 ./share/nls/en_GB.ISO8859-15 missing (created)
 ./share/nls/en_GB.US-ASCII missing (created)
 ./share/nls/en_NZ.ISO8859-1 missing (created)
 ./share/nls/en_NZ.ISO8859-15 missing (created)
 ./share/nls/en_NZ.US-ASCII missing (created)
 ./share/nls/en_US.ISO8859-1 missing (created)
 ./share/nls/en_US.ISO8859-15 missing (created)
 ./share/nls/es_ES.ISO8859-1 missing (created)
 ./share/nls/es_ES.ISO8859-15 missing (created)
 ./share/nls/et_EE.ISO8859-15 missing (created)
 ./share/nls/fi_FI.ISO8859-1 missing (created)
 ./share/nls/fi_FI.ISO8859-15 missing (created)
 ./share/nls/fr_BE.ISO8859-1 missing (created)
 ./share/nls/fr_BE.ISO8859-15 missing (created)
 ./share/nls/fr_CA.ISO8859-1 missing (created)
 ./share/nls/fr_CA.ISO8859-15 missing (created)
 ./share/nls/fr_CH.ISO8859-1 missing (created)
 ./share/nls/fr_CH.ISO8859-15 missing (created)
 ./share/nls/fr_FR.ISO8859-1 missing (created)
 ./share/nls/fr_FR.ISO8859-15 missing (created)
 ./share/nls/hi_IN.ISCII-DEV missing (created)
 ./share/nls/hr_HR.ISO8859-2 missing (created)
 ./share/nls/hu_HU.ISO8859-2 missing (created)
 ./share/nls/is_IS.ISO8859-1 missing (created)
 ./share/nls/is_IS.ISO8859-15 missing (created)
 ./share/nls/it_CH.ISO8859-1 missing (created)
 ./share/nls/it_CH.ISO8859-15 missing (created)
 ./share/nls/it_IT.ISO8859-1 missing (created)
 ./share/nls/it_IT.ISO8859-15 missing (created)
 ./share/nls/ja_JP.SJIS missing (created)
 ./share/nls/ja_JP.eucJP missing (created)
 ./share/nls/ko_KR.eucKR missing (created)
 ./share/nls/la_LN.ISO8859-1 missing (created)
 ./share/nls/la_LN.ISO8859-15 missing (created)
 ./share/nls/la_LN.ISO8859-2 missing (created)
 ./share/nls/la_LN.ISO8859-4 missing (created)
 ./share/nls/la_LN.US-ASCII missing (created)
 ./share/nls/lt_LT.ISO8859-4 missing (created)
 ./share/nls/nl_BE.ISO8859-1 missing (created)
 ./share/nls/nl_BE.ISO8859-15 missing (created)
 ./share/nls/nl_NL.ISO8859-1 missing (created)
 ./share/nls/nl_NL.ISO8859-15 missing (created)
 ./share/nls/no_NO.ISO8859-1 missing (created)
 ./share/nls/no_NO.ISO8859-15 missing (created)
 ./share/nls/pl_PL.ISO8859-2 missing (created)
 ./share/nls/pt_BR.ISO8859-1 missing (created)
 ./share/nls/pt_PT.ISO8859-1 missing (created)
 ./share/nls/pt_PT.ISO8859-15 missing (created)
 ./share/nls/ro_RO.ISO8859-2 missing (created)
 ./share/nls/ru_RU.CP866 missing (created)
 ./share/nls/ru_RU.ISO8859-5 missing (created)
 ./share/nls/ru_RU.KOI8-R missing (created)
 ./share/nls/sk_SK.ISO8859-2 missing (created)
 ./share/nls/sl_SI.ISO8859-2 missing (created)
 ./share/nls/sv_SE.ISO8859-1 missing (created)
 ./share/nls/sv_SE.ISO8859-15 missing (created)
 ./share/nls/tr_TR.ISO8859-9 missing (created)
 ./share/nls/uk_UA.ISO8859-5 missing (created)
 ./share/nls/uk_UA.KOI8-U missing (created)
 ./share/nls/zh_CN.eucCN missing (created)
 ./share/nls/zh_TW.Big5 missing (created)
 ./share/skel missing (created)
 ./var missing (created)
 ./var/cache missing (created)
 ./var/db missing (created)
 ./var/log missing (created)
 ./var/run missing (created)
 ./var/spool missing (created)
 ./www missing (created)
 xinstall: mkdir
 /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports
 .org_macports_release_tarballs_ports_R_R-
 BiocStyle/R-BiocStyle/work/destroot/opt/local/Library/Frameworks/R.framework
 xinstall: mkdir
 /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports
 .org_macports_release_tarballs_ports_R_R-
 BiocStyle/R-BiocStyle/work/destroot/opt/local/Library/Frameworks/R.framework/Versions
 xinstall: mkdir
 /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports
 .org_macports_release_tarballs_ports_R_R-
 BiocStyle/R-BiocStyle/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3
 xinstall: mkdir
 /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports
 .org_macports_release_tarballs_ports_R_R-
 BiocStyle/R-BiocStyle/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources
 xinstall: mkdir
 /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports
 .org_macports_release_tarballs_ports_R_R-
 BiocStyle/R-BiocStyle/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library
 Executing:  cd
 "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports
 .org_macports_release_tarballs_ports_R_R-
 BiocStyle/R-BiocStyle/work/BiocStyle" && /opt/local/bin/R CMD INSTALL .
 --library=/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports
 .org_macports_release_tarballs_ports_R_R-
 BiocStyle/R-BiocStyle/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library
 ERROR: dependency ‘bookdown’ is not available for package ‘BiocStyle’
 * removing
 ‘/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports
 .org_macports_release_tarballs_ports_R_R-
 BiocStyle/R-BiocStyle/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/BiocStyle’
 Command failed:  cd
 "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports
 .org_macports_release_tarballs_ports_R_R-
 BiocStyle/R-BiocStyle/work/BiocStyle" && /opt/local/bin/R CMD INSTALL .
 --library=/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports
 .org_macports_release_tarballs_ports_R_R-
 BiocStyle/R-BiocStyle/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library
 Exit code: 1
 Error: Failed to destroot R-BiocStyle: command execution failed
 }}}

 I.e. installation fails, complaining re missing R-bookdown. Now, why is it
 allegedly missing? Because it has been installed with R 4.2 and not yet
 updated, so it is broken for R. However, an update is in fact available,
 and Macports should simply update it (no, {{{-n}}} flag was not used).

 Then, I call for an update manually, and it works normally:
 {{{
 36-140% sudo port -v upgrade R-bookdown
 Warning: configured user/group macports does not exist, will build as root
 --->  Computing dependencies for R-bookdown.
 --->  Fetching distfiles for R-bookdown
 --->  bookdown_0.34.tar.gz does not exist in
 /opt/local/var/macports/distfiles/R-bookdown
 --->  Attempting to fetch bookdown_0.34.tar.gz from
 https://cran.r-project.org/src/contrib
   % Total    % Received % Xferd  Average Speed   Time    Time     Time
 Current
                                  Dload  Upload   Total   Spent    Left
 Speed
 100  838k  100  838k    0     0   318k      0  0:00:02  0:00:02 --:--:--
 318k
 --->  Verifying checksums for R-bookdown
 --->  Checksumming bookdown_0.34.tar.gz
 --->  Extracting R-bookdown
 --->  Extracting bookdown_0.34.tar.gz
 }}}

 After that, R-BiocStyle installs normally.

 Any idea why this may be the case?

-- 
Ticket URL: <https://trac.macports.org/ticket/67521>
MacPorts <https://www.macports.org/>
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