powsimR installation forces BASiCS download

[haniap]

Hello again,

I am just trying to install powsimR onto my work computer and although I already have BASiCS installed, the installation of powsimR overrides it and re-installs it again. Is there a way around this as it is creating a conflict with the various requirements of R versions? I attach the error below. With many thanks, Hania

devtools::install_github("bvieth/powsimR", build_vignettes = FALSE) Downloading GitHub repo bvieth/powsimR@master from URL https://api.github.com/repos/bvieth/powsimR/zipball/master Installing powsimR Skipping install for github remote, the SHA1 (d5d27442) has not changed since last install. Use force = TRUE to force installation Skipping install for github remote, the SHA1 (1fe6f32d) has not changed since last install. Use force = TRUE to force installation Downloading GitHub repo catavallejos/BASiCS@master from URL https://api.github.com/repos/catavallejos/BASiCS/zipball/master Installing BASiCS Skipping 1 unavailable package: SingleCellExperiment Skipping 1 package ahead of CRAN: AnnotationDbi Installing 1 package: XML trying URL 'https://cran.rstudio.com/src/contrib/XML_3.98-1.9.tar.gz' Content type 'application/x-gzip' length 1599437 bytes (1.5 MB)

downloaded 1.5 MB

• installing source package ‘XML’ ... * package ‘XML’ successfully unpacked and MD5 sums checked checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for sed... /bin/sed checking for pkg-config... /usr/bin/pkg-config checking for xml2-config... /ifs/devel/haniap/py35-v1/conda/envs/py35-v1/bin/xml2-config USE_XML2 = yes SED_EXTENDED_ARG: -E Minor 9, Patch 4 for 2.9.4 Located parser file -I/ifs/devel/haniap/py35-v1/conda/envs/py35-v1/include/libxml2 -I/ifs/devel/haniap/py35-v1/conda/envs/py35-v1/include/parser.h Checking for 1.8: -I/ifs/devel/haniap/py35-v1/conda/envs/py35-v1/include/libxml2 -I/ifs/devel/haniap/py35-v1/conda/envs/py35-v1/include Using libxml2. checking for gzopen in -lz... yes checking for xmlParseFile in -lxml2... yes You are trying to use a version 2.* edition of libxml but an incompatible library. The header files and library seem to be mismatched. If you have specified LIBXML_INCDIR, make certain to also specify an appropriate LIBXML_LIBDIR if the libxml2 library is not in the default directories. ERROR: configuration failed for package ‘XML’
• removing ‘/ifs/devel/haniap/py35-v1/conda/envs/py35-v1/lib/R/library/XML’
• restoring previous ‘/ifs/devel/haniap/py35-v1/conda/envs/py35-v1/lib/R/library/XML’

The downloaded source packages are in ‘/tmp/RtmpakBR97/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done '/ifs/devel/haniap/py35-v1/conda/envs/py35-v1/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore \ --quiet CMD INSTALL '/tmp/RtmpakBR97/devtools12d227c3df23/catavallejos-BASiCS-94c4666' \ --library='/ifs/devel/haniap/py35-v1/conda/envs/py35-v1/lib/R/library' --install-tests

ERROR: this R is version 3.3.1, package 'BASiCS' requires R >= 3.4 Error: Command failed (1) In addition: Warning message: In utils::install.packages(pkgs, repos = repos, type = type, dependencies = dependencies, : installation of package ‘XML’ had non-zero exit status

[bvieth]

Dear Hania,

thank you for your interest in powsimR.

Apparently the default setting in devtools' install_github is to install all packages listed in the dependencies. To block this unnecessary reinstallation, invoke powsimR's installation with the following command (see also the updated README):

devtools::install_github('bvieth/powsimR', build_vignettes = TRUE, dependencies=FALSE)

I hope this helps!

Best, Beate

[haniap]

Perfect - thanks Beate!