Sometimes R fails to update dependencies when a package is installed, which may break the build, if such an update is required

[barracuda156]

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?

[ryandesign (Ryan Carsten Schmidt)]

Because there is a dependency cycle; MacPorts behavior is undefined in that situation.

[ryandesign (Ryan Carsten Schmidt)]

R-BiocStyle depends directly on R-bookdown:

% port -q info --depends_lib --line r-biocstyle | tr ',' '\n' | grep -i r-bookdown
R-bookdown

but R-bookdown eventually depends on R-BiocStyle:

% echo $(port rdeps r-bookdown | grep -i r-biocstyle)
R-BiocStyle

[barracuda156]

Replying to ryandesign:

R-BiocStyle depends directly on R-bookdown:

% port -q info --depends_lib --line r-biocstyle | tr ',' '\n' | grep -i r-bookdown
R-bookdown

but R-bookdown eventually depends on R-BiocStyle:

% echo $(port rdeps r-bookdown | grep -i r-biocstyle)
R-BiocStyle

Hmm, that should not be the case, unless test dependencies are counted (what R considers suggested, or soft).

[ryandesign (Ryan Carsten Schmidt)]

Hmm, you're right, port rdeps does seem to include test dependencies, but those would only be used when running port test. When I look at only build, library, and runtime dependencies, I don't see R-BiocStyle in the rdeps of R-bookdown, so now I'm not sure what the problem is.

Next time you encounter the problem, please attach the main.log file, which should contain information about which dependencies were processed first.

[barracuda156]

Replying to ryandesign:

Hmm, you're right, port rdeps does seem to include test dependencies, but those would only be used when running port test. When I look at only build, library, and runtime dependencies, I don't see R-BiocStyle in the rdeps of R-bookdown, so now I'm not sure what the problem is.

Next time you encounter the problem, please attach the main.log file, which should contain information about which dependencies were processed first.

Okay I got another case on Rosetta.

--->  Fetching distfiles for R-rsparse
--->  rsparse-0.5.1.tar.gz does not exist in /opt/local/var/macports/distfiles/R-rsparse
--->  Attempting to fetch rsparse-0.5.1.tar.gz from http://distfiles.macports.org/R-rsparse
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  408k  100  408k    0     0  93562      0  0:00:04  0:00:04 --:--:--  117k
--->  Verifying checksums for R-rsparse
--->  Checksumming rsparse-0.5.1.tar.gz
--->  Extracting R-rsparse
--->  Extracting rsparse-0.5.1.tar.gz
Executing:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/R-rsparse/rsparse-0.5.1.tar.gz' | /usr/bin/gnutar --no-same-owner -xf - 
--->  Configuring R-rsparse
Executing:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/rsparse-0.5.1" && /opt/local/bin/R CMD build . --no-manual --no-build-vignettes 
* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘rsparse’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Removed empty directory ‘rsparse/docs’
* building ‘rsparse_0.5.1.tar.gz’

--->  Building R-rsparse
--->  Staging R-rsparse 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-rsparse/R-rsparse/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-rsparse/R-rsparse/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-rsparse/R-rsparse/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-rsparse/R-rsparse/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-rsparse/R-rsparse/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-rsparse/R-rsparse/work/rsparse-0.5.1" && /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-rsparse/R-rsparse/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library 
ERROR: dependencies ‘MatrixExtra’, ‘float’ are not available for package ‘rsparse’
* removing ‘/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/rsparse’
Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/rsparse-0.5.1" && /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-rsparse/R-rsparse/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library 
Exit code: 1
Error: Failed to destroot R-rsparse: command execution failed

Dependencies of R-rsparse in its portfile:

depends_lib-append  port:R-data.table \
                    port:R-float \
                    port:R-lgr \
                    port:R-MatrixExtra \
                    port:R-Rcpp \
                    port:R-RcppArmadillo \
                    port:R-RhpcBLASctl

compilers.setup     require_fortran

depends_test-append port:R-covr \
                    port:R-testthat

When I called after that sudo port -v upgrade R-MatrixExtra, updates proceeded:

macmini:~ svacchanda$ sudo port -v upgrade R-MatrixExtra
Password:
--->  Computing dependencies for R-float.
--->  Fetching distfiles for R-float
--->  float_0.3-1.tar.gz does not exist in /opt/local/var/macports/distfiles/R-float

Log for R-rsparse:

version:1
:debug:clean Starting logging for R-rsparse @0.5.1_1+gfortran
:debug:sysinfo Mac OS X 10.6.8 (darwin/10.8.0) arch powerpc
:debug:sysinfo MacPorts 2.8.1
:debug:sysinfo Xcode 3.2.6, CLT 1.0.0.9000000000.1.1248867338
:debug:sysinfo SDK 10.6
:debug:sysinfo MACOSX_DEPLOYMENT_TARGET: 10.6
:debug:clean Attempting ln -sf /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work /opt/local/var/macports/sources/rsync.macports.org/macports/release/tarballs/ports/R/R-rsparse/work
:debug:clean dropping privileges: euid changed to 502, egid changed to 505.
:debug:main Executing org.macports.main (R-rsparse)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:archivefetch archivefetch phase started at Sat Jun 10 06:17:02 CST 2023
:debug:archivefetch Executing proc-pre-org.macports.archivefetch-archivefetch-0
:debug:archivefetch Executing org.macports.archivefetch (R-rsparse)
:debug:archivefetch Privilege de-escalation not attempted as not running as root.
:debug:fetch fetch phase started at Sat Jun 10 06:17:02 CST 2023
:notice:fetch --->  Fetching distfiles for R-rsparse
:debug:fetch elevating privileges for fetch: euid changed to 0, egid changed to 0.
:debug:fetch dropping privileges: euid changed to 502, egid changed to 505.
:debug:fetch Executing proc-pre-org.macports.fetch-fetch-0
:debug:fetch Executing org.macports.fetch (R-rsparse)
:info:fetch --->  rsparse-0.5.1.tar.gz does not exist in /opt/local/var/macports/distfiles/R-rsparse
:notice:fetch --->  Attempting to fetch rsparse-0.5.1.tar.gz from http://distfiles.macports.org/R-rsparse
:debug:fetch Privilege de-escalation not attempted as not running as root.
:debug:checksum checksum phase started at Sat Jun 10 06:17:07 CST 2023
:notice:checksum --->  Verifying checksums for R-rsparse
:debug:checksum Executing org.macports.checksum (R-rsparse)
:info:checksum --->  Checksumming rsparse-0.5.1.tar.gz
:debug:checksum Calculated (rmd160) is 9edcd7b8417d2e62b44dcfacfb74f61f07515e3b
:debug:checksum Correct (rmd160) checksum for rsparse-0.5.1.tar.gz
:debug:checksum Calculated (sha256) is 9f57b0ab0a7bef3cad4216778a3e6d7e44037787491bcd594c12f92eefce02cf
:debug:checksum Correct (sha256) checksum for rsparse-0.5.1.tar.gz
:debug:checksum Calculated (size) is 417799
:debug:checksum Correct (size) checksum for rsparse-0.5.1.tar.gz
:debug:checksum Privilege de-escalation not attempted as not running as root.
:debug:extract extract phase started at Sat Jun 10 06:17:07 CST 2023
:notice:extract --->  Extracting R-rsparse
:debug:extract Executing org.macports.extract (R-rsparse)
:info:extract --->  Extracting rsparse-0.5.1.tar.gz
:debug:extract setting option extract.args to '/opt/local/var/macports/distfiles/R-rsparse/rsparse-0.5.1.tar.gz'
:debug:extract Environment: 
:debug:extract CC_PRINT_OPTIONS='YES'
:debug:extract CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/.CC_PRINT_OPTIONS'
:debug:extract CPATH='/opt/local/include'
:debug:extract DEVELOPER_DIR='/Developer'
:debug:extract LIBRARY_PATH='/opt/local/lib'
:debug:extract MACOSX_DEPLOYMENT_TARGET='10.6'
:info:extract Executing:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/R-rsparse/rsparse-0.5.1.tar.gz' | /usr/bin/gnutar --no-same-owner -xf - 
:debug:extract system:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work" && /usr/bin/gzip -dc '/opt/local/var/macports/distfiles/R-rsparse/rsparse-0.5.1.tar.gz' | /usr/bin/gnutar --no-same-owner -xf - 
:debug:extract euid/egid changed to: 0/0
:debug:extract chowned /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work to macports
:debug:extract euid/egid changed to: 502/505
:debug:extract extract.rename: Renaming rexyai-rsparse-3ecd3cd -> rsparse-0.5.1
:debug:extract Privilege de-escalation not attempted as not running as root.
:debug:patch patch phase started at Sat Jun 10 06:17:07 CST 2023
:debug:patch Executing org.macports.patch (R-rsparse)
:debug:patch Privilege de-escalation not attempted as not running as root.
:debug:configure configure phase started at Sat Jun 10 06:17:07 CST 2023
:notice:configure --->  Configuring R-rsparse
:debug:configure Preferred compilers: macports-gcc-12 macports-gcc-11 macports-gcc-10 macports-gcc-9 macports-gcc-8 macports-gcc-7 macports-gcc-6 macports-gcc-5 macports-clang-11 macports-clang-10 macports-clang-9.0 macports-clang-8.0 macports-clang-7.0 macports-clang-6.0 macports-clang-5.0
:debug:configure Using compiler 'MacPorts GCC 12'
:debug:configure Executing proc-pre-org.macports.configure-configure-0
:debug:configure Active variants check for source-type install considers depends_fetch depends_extract depends_lib depends_build depends_run: R-data.table R-float R-lgr R-MatrixExtra R-Rcpp R-RcppArmadillo R-RhpcBLASctl libgcc gcc12 R
:debug:configure R is installed with the following variants: +builtin_lapack+cairo+gcc12+openmp+recommended+tcltk+x11
:debug:configure   required: recommended, forbidden: 
:debug:configure   accepted
:debug:configure Executing proc-pre-org.macports.configure-configure-1
:debug:configure compilers.enforce_c list: 
:debug:configure compilers.enforce_fortran list: 
:debug:configure compilers.enforce_some_fortran list: 
:debug:configure Executing org.macports.configure (R-rsparse)
:debug:configure Environment: 
:debug:configure CC='/opt/local/bin/gcc-mp-12'
:debug:configure CC_PRINT_OPTIONS='YES'
:debug:configure CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/.CC_PRINT_OPTIONS'
:debug:configure CFLAGS='-pipe -Os -arch ppc'
:debug:configure CPATH='/opt/local/include'
:debug:configure CPPFLAGS='-I/opt/local/include'
:debug:configure CXX='/opt/local/bin/g++-mp-12'
:debug:configure CXXFLAGS='-pipe -Os -D_GLIBCXX_USE_CXX11_ABI=0 -arch ppc'
:debug:configure DEVELOPER_DIR='/Developer'
:debug:configure DYLD_LIBRARY_PATH='/opt/local/lib/libgcc'
:debug:configure F77='/opt/local/bin/gfortran-mp-12'
:debug:configure F90='/opt/local/bin/gfortran-mp-12'
:debug:configure F90FLAGS='-pipe -Os -m32'
:debug:configure FC='/opt/local/bin/gfortran-mp-12'
:debug:configure FCFLAGS='-pipe -Os -m32'
:debug:configure FFLAGS='-pipe -Os -m32'
:debug:configure INSTALL='/usr/bin/install -c'
:debug:configure LDFLAGS='-L/opt/local/lib -Wl,-headerpad_max_install_names -Wl,-rpath,/opt/local/lib/libgcc -arch ppc'
:debug:configure LIBRARY_PATH='/opt/local/lib'
:debug:configure MACOSX_DEPLOYMENT_TARGET='10.6'
:debug:configure OBJC='/opt/local/bin/gcc-mp-12'
:debug:configure OBJCFLAGS='-pipe -Os -arch ppc'
:debug:configure OBJCXX='/opt/local/bin/g++-mp-12'
:debug:configure OBJCXXFLAGS='-pipe -Os -D_GLIBCXX_USE_CXX11_ABI=0 -arch ppc'
:info:configure Executing:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/rsparse-0.5.1" && /opt/local/bin/R CMD build . --no-manual --no-build-vignettes 
:debug:configure system:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/rsparse-0.5.1" && /opt/local/bin/R CMD build . --no-manual --no-build-vignettes 
:info:configure * checking for file ‘./DESCRIPTION’ ... OK
:info:configure * preparing ‘rsparse’:
:info:configure * checking DESCRIPTION meta-information ... OK
:info:configure * cleaning src
:info:configure * running ‘cleanup’
:info:configure * checking for LF line-endings in source and make files and shell scripts
:info:configure * checking for empty or unneeded directories
:info:configure Removed empty directory ‘rsparse/docs’
:info:configure * building ‘rsparse_0.5.1.tar.gz’
:debug:configure Executing portconfigure::configure_finish
:debug:configure Privilege de-escalation not attempted as not running as root.
:debug:build build phase started at Sat Jun 10 06:17:11 CST 2023
:notice:build --->  Building R-rsparse
:debug:build Executing org.macports.build (R-rsparse)
:debug:build Privilege de-escalation not attempted as not running as root.
:debug:destroot destroot phase started at Sat Jun 10 06:17:11 CST 2023
:notice:destroot --->  Staging R-rsparse into destroot
:debug:destroot Can't run destroot under sudo without elevated privileges (due to mtree).
:debug:destroot Run destroot without sudo to avoid root privileges.
:debug:destroot Going to escalate privileges back to root.
:debug:destroot euid changed to: 0. egid changed to: 0.
:debug:destroot system -W /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/destroot: /usr/sbin/mtree -e -U -f /opt/local/share/macports/install/macosx.mtree
:info:destroot . changed
:info:destroot 	gid expected 0 found 80 modified
:info:destroot ./usr missing (created)
:info:destroot . missing (directory not created: File exists)
:info:destroot ./Applications missing (created)
:info:destroot ./Developer missing (created)
:info:destroot ./Library missing (created)
:debug:destroot system -W /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/destroot/opt/local: /usr/sbin/mtree -e -U -f /opt/local/share/macports/install/prefix.mtree
:info:destroot . changed
:info:destroot 	gid expected 80 found 0 modified
:info:destroot ./bin missing (created)
:info:destroot ./etc missing (created)
:info:destroot ./include missing (created)
:info:destroot ./lib missing (created)
:info:destroot ./lib/pkgconfig missing (created)
:info:destroot ./libexec missing (created)
:info:destroot ./sbin missing (created)
:info:destroot ./share missing (created)
:info:destroot ./share/doc missing (created)
:info:destroot ./share/info missing (created)
:info:destroot ./share/man missing (created)
:info:destroot ./share/man/cat1 missing (created)
:info:destroot ./share/man/cat2 missing (created)
:info:destroot ./share/man/cat3 missing (created)
:info:destroot ./share/man/cat4 missing (created)
:info:destroot ./share/man/cat5 missing (created)
:info:destroot ./share/man/cat6 missing (created)
:info:destroot ./share/man/cat7 missing (created)
:info:destroot ./share/man/cat8 missing (created)
:info:destroot ./share/man/cat9 missing (created)
:info:destroot ./share/man/catl missing (created)
:info:destroot ./share/man/catn missing (created)
:info:destroot ./share/man/man1 missing (created)
:info:destroot ./share/man/man2 missing (created)
:info:destroot ./share/man/man3 missing (created)
:info:destroot ./share/man/man4 missing (created)
:info:destroot ./share/man/man5 missing (created)
:info:destroot ./share/man/man6 missing (created)
:info:destroot ./share/man/man7 missing (created)
:info:destroot ./share/man/man8 missing (created)
:info:destroot ./share/man/man9 missing (created)
:info:destroot ./share/man/manl missing (created)
:info:destroot ./share/man/mann missing (created)
:info:destroot ./share/nls missing (created)
:info:destroot ./share/nls/C missing (created)
:info:destroot ./share/nls/af_ZA.ISO8859-1 missing (created)
:info:destroot ./share/nls/af_ZA.ISO8859-15 missing (created)
:info:destroot ./share/nls/bg_BG.CP1251 missing (created)
:info:destroot ./share/nls/cs_CZ.ISO8859-2 missing (created)
:info:destroot ./share/nls/da_DK.ISO8859-1 missing (created)
:info:destroot ./share/nls/da_DK.ISO8859-15 missing (created)
:info:destroot ./share/nls/de_AT.ISO8859-1 missing (created)
:info:destroot ./share/nls/de_AT.ISO8859-15 missing (created)
:info:destroot ./share/nls/de_CH.ISO8859-1 missing (created)
:info:destroot ./share/nls/de_CH.ISO8859-15 missing (created)
:info:destroot ./share/nls/de_DE.ISO8859-1 missing (created)
:info:destroot ./share/nls/de_DE.ISO8859-15 missing (created)
:info:destroot ./share/nls/el_GR.ISO8859-7 missing (created)
:info:destroot ./share/nls/en_AU.ISO8859-1 missing (created)
:info:destroot ./share/nls/en_AU.ISO8859-15 missing (created)
:info:destroot ./share/nls/en_AU.US-ASCII missing (created)
:info:destroot ./share/nls/en_CA.ISO8859-1 missing (created)
:info:destroot ./share/nls/en_CA.ISO8859-15 missing (created)
:info:destroot ./share/nls/en_CA.US-ASCII missing (created)
:info:destroot ./share/nls/en_GB.ISO8859-1 missing (created)
:info:destroot ./share/nls/en_GB.ISO8859-15 missing (created)
:info:destroot ./share/nls/en_GB.US-ASCII missing (created)
:info:destroot ./share/nls/en_NZ.ISO8859-1 missing (created)
:info:destroot ./share/nls/en_NZ.ISO8859-15 missing (created)
:info:destroot ./share/nls/en_NZ.US-ASCII missing (created)
:info:destroot ./share/nls/en_US.ISO8859-1 missing (created)
:info:destroot ./share/nls/en_US.ISO8859-15 missing (created)
:info:destroot ./share/nls/es_ES.ISO8859-1 missing (created)
:info:destroot ./share/nls/es_ES.ISO8859-15 missing (created)
:info:destroot ./share/nls/et_EE.ISO8859-15 missing (created)
:info:destroot ./share/nls/fi_FI.ISO8859-1 missing (created)
:info:destroot ./share/nls/fi_FI.ISO8859-15 missing (created)
:info:destroot ./share/nls/fr_BE.ISO8859-1 missing (created)
:info:destroot ./share/nls/fr_BE.ISO8859-15 missing (created)
:info:destroot ./share/nls/fr_CA.ISO8859-1 missing (created)
:info:destroot ./share/nls/fr_CA.ISO8859-15 missing (created)
:info:destroot ./share/nls/fr_CH.ISO8859-1 missing (created)
:info:destroot ./share/nls/fr_CH.ISO8859-15 missing (created)
:info:destroot ./share/nls/fr_FR.ISO8859-1 missing (created)
:info:destroot ./share/nls/fr_FR.ISO8859-15 missing (created)
:info:destroot ./share/nls/hi_IN.ISCII-DEV missing (created)
:info:destroot ./share/nls/hr_HR.ISO8859-2 missing (created)
:info:destroot ./share/nls/hu_HU.ISO8859-2 missing (created)
:info:destroot ./share/nls/is_IS.ISO8859-1 missing (created)
:info:destroot ./share/nls/is_IS.ISO8859-15 missing (created)
:info:destroot ./share/nls/it_CH.ISO8859-1 missing (created)
:info:destroot ./share/nls/it_CH.ISO8859-15 missing (created)
:info:destroot ./share/nls/it_IT.ISO8859-1 missing (created)
:info:destroot ./share/nls/it_IT.ISO8859-15 missing (created)
:info:destroot ./share/nls/ja_JP.SJIS missing (created)
:info:destroot ./share/nls/ja_JP.eucJP missing (created)
:info:destroot ./share/nls/ko_KR.eucKR missing (created)
:info:destroot ./share/nls/la_LN.ISO8859-1 missing (created)
:info:destroot ./share/nls/la_LN.ISO8859-15 missing (created)
:info:destroot ./share/nls/la_LN.ISO8859-2 missing (created)
:info:destroot ./share/nls/la_LN.ISO8859-4 missing (created)
:info:destroot ./share/nls/la_LN.US-ASCII missing (created)
:info:destroot ./share/nls/lt_LT.ISO8859-4 missing (created)
:info:destroot ./share/nls/nl_BE.ISO8859-1 missing (created)
:info:destroot ./share/nls/nl_BE.ISO8859-15 missing (created)
:info:destroot ./share/nls/nl_NL.ISO8859-1 missing (created)
:info:destroot ./share/nls/nl_NL.ISO8859-15 missing (created)
:info:destroot ./share/nls/no_NO.ISO8859-1 missing (created)
:info:destroot ./share/nls/no_NO.ISO8859-15 missing (created)
:info:destroot ./share/nls/pl_PL.ISO8859-2 missing (created)
:info:destroot ./share/nls/pt_BR.ISO8859-1 missing (created)
:info:destroot ./share/nls/pt_PT.ISO8859-1 missing (created)
:info:destroot ./share/nls/pt_PT.ISO8859-15 missing (created)
:info:destroot ./share/nls/ro_RO.ISO8859-2 missing (created)
:info:destroot ./share/nls/ru_RU.CP866 missing (created)
:info:destroot ./share/nls/ru_RU.ISO8859-5 missing (created)
:info:destroot ./share/nls/ru_RU.KOI8-R missing (created)
:info:destroot ./share/nls/sk_SK.ISO8859-2 missing (created)
:info:destroot ./share/nls/sl_SI.ISO8859-2 missing (created)
:info:destroot ./share/nls/sv_SE.ISO8859-1 missing (created)
:info:destroot ./share/nls/sv_SE.ISO8859-15 missing (created)
:info:destroot ./share/nls/tr_TR.ISO8859-9 missing (created)
:info:destroot ./share/nls/uk_UA.ISO8859-5 missing (created)
:info:destroot ./share/nls/uk_UA.KOI8-U missing (created)
:info:destroot ./share/nls/zh_CN.eucCN missing (created)
:info:destroot ./share/nls/zh_TW.Big5 missing (created)
:info:destroot ./share/skel missing (created)
:info:destroot ./var missing (created)
:info:destroot ./var/cache missing (created)
:info:destroot ./var/db missing (created)
:info:destroot ./var/log missing (created)
:info:destroot ./var/run missing (created)
:info:destroot ./var/spool missing (created)
:info:destroot ./www missing (created)
:debug:destroot Executing proc-pre-org.macports.destroot-destroot-0
:info:destroot xinstall: mkdir /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/destroot/opt/local/Library/Frameworks/R.framework
:info:destroot xinstall: mkdir /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/destroot/opt/local/Library/Frameworks/R.framework/Versions
:info:destroot xinstall: mkdir /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3
:info:destroot xinstall: mkdir /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources
:info:destroot xinstall: mkdir /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library
:debug:destroot Executing org.macports.destroot (R-rsparse)
:debug:destroot Environment: 
:debug:destroot CC_PRINT_OPTIONS='YES'
:debug:destroot CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/.CC_PRINT_OPTIONS'
:debug:destroot CPATH='/opt/local/include'
:debug:destroot DEVELOPER_DIR='/Developer'
:debug:destroot DYLD_LIBRARY_PATH='/opt/local/lib/libgcc'
:debug:destroot LIBRARY_PATH='/opt/local/lib'
:debug:destroot MACOSX_DEPLOYMENT_TARGET='10.6'
:info:destroot Executing:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/rsparse-0.5.1" && /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-rsparse/R-rsparse/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library 
:debug:destroot system:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/rsparse-0.5.1" && /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-rsparse/R-rsparse/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library 
:info:destroot ERROR: dependencies ‘MatrixExtra’, ‘float’ are not available for package ‘rsparse’
:info:destroot * removing ‘/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library/rsparse’
:info:destroot Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/work/rsparse-0.5.1" && /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-rsparse/R-rsparse/work/destroot/opt/local/Library/Frameworks/R.framework/Versions/4.3/Resources/library 
:info:destroot Exit code: 1
:error:destroot Failed to destroot R-rsparse: command execution failed
:debug:destroot Error code: CHILDSTATUS 13758 1
:debug:destroot Backtrace: command execution failed
:debug:destroot     while executing
:debug:destroot "system {*}$notty {*}$callback {*}$nice $fullcmdstring"
:debug:destroot     invoked from within
:debug:destroot "command_exec -callback portprogress::target_progress_callback destroot"
:debug:destroot     (procedure "portdestroot::destroot_main" line 2)
:debug:destroot     invoked from within
:debug:destroot "$procedure $targetname"
:error:destroot See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_R_R-rsparse/R-rsparse/main.log for details.