Hi everyone,
we're currently in the process of build out our RStudio Connect instance at work and deployment goes well until it attempts to install the xml2 package.
[Connect] 2021/06/16 13:42:18.765221386 [1] "Command failed (1)\n\nFailed to run system command:\n\n\t'/usr/local/lib/R/bin/R' --vanilla CMD INSTALL --preclean '/opt/rstudio-connect/mnt/tmp/RtmpbG7MvM/packrat-install-6dc127ffc4a8/xml2' --library='/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.4' --install-tests --no-docs --no-multiarch --no-demo \n\nThe command failed with output:\n* installing *source* package ‘xml2’ ...\n** package ‘xml2’ successfully unpacked and MD5 sums checked\n** using staged installation\nFound pkg-config cflags and libs!\nUsing PKG_CFLAGS=-I/usr/include/libxml2\nUsing PKG_LIBS=-lxml2\n** libs\ng++ -std=gnu++11 -I\"/usr/local/lib/R/include\" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c connection.cpp -o connection.o\ngcc -I\"/usr/local/lib/R/include\" -DNDEBUG -I../inst/include -I/usr/include
[Connect] /libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o\ng++ -std=gnu++11 -I\"/usr/local/lib/R/include\" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xml2_doc.cpp -o xml2_doc.o\ng++ -std=gnu++11 -I\"/usr/local/lib/R/include\" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xml2_init.cpp -o xml2_init.o\ng++ -std=gnu++11 -I\"/usr/local/lib/R/include\" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wd
[Connect] ate-time -D_FORTIFY_SOURCE=2 -g -c xml2_namespace.cpp -o xml2_namespace.o\ng++ -std=gnu++11 -I\"/usr/local/lib/R/include\" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xml2_node.cpp -o xml2_node.o\ng++ -std=gnu++11 -I\"/usr/local/lib/R/include\" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xml2_output.cpp -o xml2_output.o\ng++ -std=gnu++11 -I\"/usr/local/lib/R/include\" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xml2_schema.cpp -o xml2_schema.o\ng++ -std=gnu++11 -I\"/usr/local
[Connect] /lib/R/include\" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xml2_url.cpp -o xml2_url.o\ng++ -std=gnu++11 -I\"/usr/local/lib/R/include\" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xml2_xpath.cpp -o xml2_xpath.o\ng++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o xml2.so connection.o init.o xml2_doc.o xml2_init.o xml2_namespace.o xml2_node.o xml2_output.o xml2_schema.o xml2_url.o xml2_xpath.o -lxml2 -L/usr/local/lib/R/lib -lR\ninstalling to /opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.4/00LOCK-xml2/00new/xml2/libs\n** R\n** inst\n** tests\n** byte-compile and prepare package for lazy loading\n** help\n*** installing h
[Connect] elp indices\n** building package indices\n** installing vignettes\n** testing if installed package can be loaded from temporary location\n** checking absolute paths in shared objects and dynamic libraries\nmv: cannot move '/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.4/00LOCK-xml2/00new/xml2' to '/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.4/xml2': Permission denied\nERROR: moving to final location failed"
[Connect] 2021/06/16 13:42:18.803014150 Error: Command failed (1)
[Connect] 2021/06/16 13:42:18.803017350
[Connect] 2021/06/16 13:42:18.803047952 Failed to run system command:
[Connect] 2021/06/16 13:42:18.803048852
[Connect] 2021/06/16 13:42:18.803054853 '/usr/local/lib/R/bin/R' --vanilla CMD INSTALL --preclean '/opt/rstudio-connect/mnt/tmp/RtmpbG7MvM/packrat-install-6dc127ffc4a8/xml2' --library='/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.4' --install-tests --no-docs --no-multiarch --no-demo
[Connect] 2021/06/16 13:42:18.803060753
[Connect] 2021/06/16 13:42:18.803067153 The command failed with output:
[Connect] 2021/06/16 13:42:18.803067753 * installing *source* package ‘xml2’ ...
[Connect] 2021/06/16 13:42:18.803074754 ** package ‘xml2’ successfully unpacked and MD5 sums checked
[Connect] 2021/06/16 13:42:18.803075554 ** using staged installation
[Connect] 2021/06/16 13:42:18.803084054 Found pkg-config cflags and libs!
[Connect] 2021/06/16 13:42:18.803084755 Using PKG_CFLAGS=-I/usr/include/libxml2
[Connect] 2021/06/16 13:42:18.803108156 Using PKG_LIBS=-lxml2
[Connect] 2021/06/16 13:42:18.803109156 ** libs
[Connect] 2021/06/16 13:42:18.803115657 g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c connection.cpp -o connection.o
[Connect] 2021/06/16 13:42:18.803119457 gcc -I"/usr/local/lib/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
[Connect] 2021/06/16 13:42:18.803128557 g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xml2_doc.cpp -o xml2_doc.o
[Connect] 2021/06/16 13:42:18.803129157 g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xml2_init.cpp -o xml2_init.o
[Connect] 2021/06/16 13:42:18.803135158 g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xml2_namespace.cpp -o xml2_namespace.o
[Connect] 2021/06/16 13:42:18.803135558 g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xml2_node.cpp -o xml2_node.o
[Connect] 2021/06/16 13:42:18.803143458 g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xml2_output.cpp -o xml2_output.o
[Connect] 2021/06/16 13:42:18.803144058 g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xml2_schema.cpp -o xml2_schema.o
[Connect] 2021/06/16 13:42:18.803149859 g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xml2_url.cpp -o xml2_url.o
[Connect] 2021/06/16 13:42:18.803150259 g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xml2_xpath.cpp -o xml2_xpath.o
[Connect] 2021/06/16 13:42:18.803163760 g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o xml2.so connection.o init.o xml2_doc.o xml2_init.o xml2_namespace.o xml2_node.o xml2_output.o xml2_schema.o xml2_url.o xml2_xpath.o -lxml2 -L/usr/local/lib/R/lib -lR
[Connect] 2021/06/16 13:42:18.803164260 installing to /opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.4/00LOCK-xml2/00new/xml2/libs
[Connect] 2021/06/16 13:42:18.803170760 ** R
[Connect] 2021/06/16 13:42:18.803171260 ** inst
[Connect] 2021/06/16 13:42:18.803177361 ** tests
[Connect] 2021/06/16 13:42:18.803177861 ** byte-compile and prepare package for lazy loading
[Connect] 2021/06/16 13:42:18.803186161 ** help
[Connect] 2021/06/16 13:42:18.803186861 *** installing help indices
[Connect] 2021/06/16 13:42:18.803192962 ** building package indices
[Connect] 2021/06/16 13:42:18.803193462 ** installing vignettes
[Connect] 2021/06/16 13:42:18.803201462 ** testing if installed package can be loaded from temporary location
[Connect] 2021/06/16 13:42:18.803202262 ** checking absolute paths in shared objects and dynamic libraries
[Connect] 2021/06/16 13:42:18.803208963 mv: cannot move '/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.4/00LOCK-xml2/00new/xml2' to '/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/4.0.4/xml2': Permission denied
[Connect] 2021/06/16 13:42:18.803212063 ERROR: moving to final location failed
[Connect] 2021/06/16 13:42:18.803218463
[Connect] 2021/06/16 13:42:18.803219063 Unable to fully restore the R packages associated with this deployment.
[Connect] 2021/06/16 13:42:18.803225164 Please review the preceding messages to determine which package
[Connect] 2021/06/16 13:42:18.803225964 encountered installation difficulty and the cause of the failure.
[Connect] 2021/06/16 13:42:18.821665166 Warning message:
[Connect] 2021/06/16 13:42:18.821668366 In packrat::restore(overwrite.dirty = TRUE, prompt = FALSE, restart = FALSE) :
[Connect] 2021/06/16 13:42:18.821685867 The most recent snapshot was generated using R version 4.0.2
[Connect] Build error: exit status 1
I've cleared the lock file but I everytime I re-attempt to deploy it happens again. I haven't yet encountered this with any other package and have deployed other apps succesfully.
Any help appreciated on this.
Cheers,
Andy P.