############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpectriPy ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘SpectriPy’ ... ** this is package ‘SpectriPy’ version ‘1.0.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location python: /Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/nGjcgFjVxO3au43UlFV3w/bin/python libpython: /Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/python/cpython-3.12.11-macos-aarch64-none/lib/libpython3.12.dylib pythonhome: /Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/nGjcgFjVxO3au43UlFV3w:/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/nGjcgFjVxO3au43UlFV3w virtualenv: /Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/nGjcgFjVxO3au43UlFV3w/bin/activate_this.py version: 3.12.11 (main, Jul 11 2025, 22:26:01) [Clang 20.1.4 ] numpy: /Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/nGjcgFjVxO3au43UlFV3w/lib/python3.12/site-packages/numpy numpy_version: 2.2.6 NOTE: Python version was forced by py_require() BBS_BIOC_GIT_BRANCH RELEASE_3_22 BBS_BIOC_MANIFEST_CLONE_PATH /Users/biocbuild/bbs-3.22-bioc/manifest BBS_BIOC_MANIFEST_FILE software.txt BBS_BIOC_MANIFEST_GIT_BRANCH RELEASE_3_22 BBS_BIOC_MANIFEST_GIT_REPO_URL https://git.bioconductor.org/admin/manifest BBS_BIOC_VERSION 3.22 BBS_BIOC_VERSIONED_REPO_PATH 3.22/bioc BBS_BUILDTYPE bioc BBS_BUILD_NB_CPU 13 BBS_CENTRAL_BASEURL http://149.165.152.87/BBS/3.22/bioc BBS_CENTRAL_RDIR /home/biocbuild/public_html/BBS/3.22/bioc BBS_CENTRAL_RHOST bbscentral2 BBS_CENTRAL_ROOT_URL http://149.165.152.87 BBS_CENTRAL_RUSER biocbuild BBS_CHECK_NB_CPU 14 BBS_CURL_CMD /usr/bin/curl BBS_DEBUG 0 BBS_EXTRA_CHECK_OPTIONS --no-vignettes BBS_GITLOG_PATH /Users/biocbuild/bbs-3.22-bioc/gitlog BBS_GITLOG_RDIR /home/biocbuild/public_html/BBS/3.22/bioc/gitlog BBS_GITLOG_RHOST bbscentral2 BBS_GITLOG_RUSER biocbuild BBS_HOME /Users/biocbuild/BBS BBS_MEAT0_RDIR /home/biocbuild/bbs-3.22-bioc/MEAT0 BBS_MEAT0_RHOST bbscentral2 BBS_MEAT0_RUSER biocbuild BBS_MEAT0_TYPE 3 BBS_MEAT_PATH /Users/biocbuild/bbs-3.22-bioc/meat BBS_NB_CPU 15 BBS_NODE_HOSTNAME kjohnson3 BBS_NON_TARGET_REPOS_FILE /Users/biocbuild/BBS/3.22/bioc/non_target_repos.txt BBS_PRODUCT_TRANSMISSION_MODE asynchronous BBS_PYTHON_CMD /usr/bin/python3 BBS_RSCRIPT_CMD /Library/Frameworks/R.framework/Resources/bin/Rscript BBS_RSH_CMD ssh -F /Users/biocbuild/.ssh/config BBS_RSYNC_CMD /usr/bin/rsync BBS_RSYNC_OPTIONS -rl --delete --delete-excluded --exclude='.svn' --exclude='.git' --exclude='.github' --exclude='.git_*' BBS_RSYNC_RSH_CMD /usr/bin/rsync --rsh 'ssh -F /Users/biocbuild/.ssh/config' BBS_R_CMD /Library/Frameworks/R.framework/Resources/bin/R BBS_R_HOME /Library/Frameworks/R.framework/Resources BBS_SSH_CMD /usr/bin/ssh BBS_TAR_CMD /usr/bin/tar BBS_UPDATE_MEAT0 1 BBS_USER biocbuild BBS_WORK_TOPDIR /Users/biocbuild/bbs-3.22-bioc BIBINPUTS .:/Library/Frameworks/R.framework/Resources/share/texmf/bibtex/bib: BIOCPARALLEL_WORKER_NUMBER 4 BLAST_USAGE_REPORT false BSTINPUTS .:/Library/Frameworks/R.framework/Resources/share/texmf/bibtex/bst: DISPLAY :1.0 DONT_PUSH_SRCPKGS 1 DYLD_FALLBACK_LIBRARY_PATH /Library/Frameworks/R.framework/Resources/lib:/usr/local/jdk-21.jdk/Contents/Home/lib/server EDITOR vi HOME /Users/biocbuild HOMEBREW_CELLAR /opt/homebrew/Cellar HOMEBREW_PREFIX /opt/homebrew HOMEBREW_REPOSITORY /opt/homebrew INFOPATH /opt/homebrew/share/info:/opt/homebrew/share/info: IS_BIOC_BUILD_MACHINE true JAVA_HOME /usr/local/jdk-21.jdk/Contents/Home KMP_DEVICE_THREAD_LIMIT 2 KMP_TEAMS_THREAD_LIMIT 2 LANG en_US.UTF-8 LC_COLLATE C LC_TIME en_GB LN_S ln -s LOGNAME biocbuild MACOSX_DEPLOYMENT_TARGET 11.0 MAKE make MANPATH /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/share/man:/Library/Developer/CommandLineTools/usr/share/man:/Library/Developer/CommandLineTools/Toolchains/XcodeDefault.xctoolchain/usr/share/man: OMP_NUM_THREADS 2 OMP_THREAD_LIMIT 2 OPENSSL_LIBS /opt/R/arm64/lib/libssl.a /opt/R/arm64/lib/libcrypto.a PAGER /usr/bin/less PATH /Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/nGjcgFjVxO3au43UlFV3w/bin:/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/nGjcgFjVxO3au43UlFV3w/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/Applications/CMake.app/Contents/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/usr/local/ncbi/igblast/bin:/usr/local/share/dotnet:/opt/salt:/opt/X11/bin:/Applications/quarto/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Users/biocbuild/.cargo/bin:/opt/gfortran/bin:/opt/R/arm64/bin PKG_CONFIG_PATH :/usr/local/lib/openbabel3/pkgconfig:/opt/R/arm64/lib/pkgconfig:/usr/local/lib/openbabel3/pkgconfig:/opt/R/arm64/lib/pkgconfig PWD /Users/biocbuild/bbs-3.22-bioc/meat/SpectriPy PYTHONPATH RDBASE /Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/nGjcgFjVxO3au43UlFV3w/lib/python3.12/site-packages/rdkit RETICULATE_USE_MANAGED_VENV yes RGL_USE_NULL TRUE R_ARCH R_BROWSER /usr/bin/open R_BZIPCMD /usr/bin/bzip2 R_CMD /Library/Frameworks/R.framework/Resources/bin/Rcmd R_DEFAULT_INTERNET_TIMEOUT 600 R_DEFAULT_PACKAGES R_DOC_DIR /Library/Frameworks/R.framework/Resources/doc R_ENVIRON_USER /Users/biocbuild/BBS/3.22/Renviron.bioc R_GZIPCMD /usr/bin/gzip R_HOME /Library/Frameworks/R.framework/Resources R_INCLUDE_DIR /Library/Frameworks/R.framework/Resources/include R_INSTALL_PKG SpectriPy R_LIBRARY_DIR /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library R_LIBS /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-SpectriPy/00new R_LIBS_SITE /Library/Frameworks/R.framework/Resources/site-library R_LIBS_USER /Users/biocbuild/Library/R/arm64/4.5/library R_OSTYPE unix R_PACKAGE_DIR /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-SpectriPy/00new/SpectriPy R_PACKAGE_NAME SpectriPy R_PAPERSIZE a4 R_PAPERSIZE_USER a4 R_PDFVIEWER /usr/bin/open R_PLATFORM aarch64-apple-darwin20 R_PRINTCMD lpr R_QPDF /Library/Frameworks/R.framework/Resources/bin/qpdf R_RD4PDF times,inconsolata,hyper R_SESSION_INITIALIZED PID=9545:NAME="reticulate" R_SESSION_TMPDIR /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKJ7Rqt R_SHARE_DIR /Library/Frameworks/R.framework/Resources/share R_STRIP_SHARED_LIB strip -x R_STRIP_STATIC_LIB strip -S R_TESTS R_TEXI2DVICMD /opt/R/arm64/bin/texi2dvi R_UNZIPCMD /usr/bin/unzip R_VERSION 4.5.1 R_ZIPCMD /usr/bin/zip SDKROOT /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk SED /usr/bin/sed SHELL /bin/bash SHLVL 6 SSH_AUTH_SOCK /tmp/ssh-bIwEKsfqDN/agent.21773 SSH_CLIENT 155.52.47.40 59200 22 SSH_CONNECTION 155.52.47.40 59200 172.24.216.75 22 SSH_TTY /dev/ttys005 TAR /usr/bin/tar TERM xterm-256color TEXINPUTS .:/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex: TMPDIR /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/ USER biocbuild VIRTUAL_ENV /Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/nGjcgFjVxO3au43UlFV3w VIRTUAL_ENV_PROMPT nGjcgFjVxO3au43UlFV3w _R_CHECK_EXCESSIVE_IMPORTS_ 20 _R_CHECK_EXECUTABLES_ false _R_CHECK_EXECUTABLES_EXCLUSIONS_ false _R_CHECK_LENGTH_1_CONDITION_ package:_R_CHECK_PACKAGE_NAME_,abort,verbose _R_CHECK_LENGTH_1_LOGIC2_ package:_R_CHECK_PACKAGE_NAME_,abort,verbose _R_CHECK_NEWS_IN_PLAIN_TEXT_ true _R_CHECK_S3_METHODS_NOT_REGISTERED_ true _R_CHECK_SUGGESTS_ONLY_ true _R_CHECK_XREFS_MIND_SUSPECT_ANCHORS_ true _R_CHECK_XREFS_NOTE_MISSING_PACKAGE_ANCHORS_ true _R_COMPARE_LANG_OBJECTS eqonly _R_CXX_USE_NO_REMAP_ true _R_USE_STRICT_R_HEADERS_ true __CF_USER_TEXT_ENCODING 0x1FA:0:0 Error: package or namespace load failed for ‘SpectriPy’: .onLoad failed in loadNamespace() for 'SpectriPy', details: call: value[[3L]](cond) error: Failed to initialize Python environment and libraries! Original message: Could not find/load shared object file Python configuration: Environmental variables: RELEASE_3_22/Users/biocbuild/bbs-3.22-bioc/manifestsoftware.txtRELEASE_3_22https://git.bioconductor.org/admin/manifest3.223.22/biocbioc13http://149.165.152.87/BBS/3.22/bioc/home/biocbuild/public_html/BBS/3.22/biocbbscentral2http://149.165.152.87biocbuild14/usr/bin/curl0--no-vignettes/Users/biocbuild/bbs-3.22-bioc/gitlog/home/biocbuild/public_html/BBS/3.22/bioc/gitlogbbscentral2biocbuild/Users/biocbuild/BBS/home/biocbuild/bbs-3.22-bioc/MEAT0bbscentral2biocbuild3/Users/biocbuild/bbs-3.22-bioc/meat15kjohnson3/Users/biocbuild/BBS/3.22/bioc/non_target_repos.txtasynchronous/usr/bin/python3/Library/Frameworks/R.framework/Resources/bin/Rscriptssh -F /Users/biocbuild/.ssh/config/usr/bin/rsync-rl --delete --delete-excluded --exclude='.svn' --exclude='.git' --exclude='.github' --exclude='.git_*'/usr/bin/rsync --rsh 'ssh -F /Users/biocbuild/.ssh/config'/Library/Frameworks/R.framework/Resources/bin/R/Library/Frameworks/R.framework/Resources/usr/bin/ssh/usr/bin/tar1biocbuild/Users/biocbuild/bbs-3.22-bioc.:/Library/Frameworks/R.framework/Resources/share/texmf/bibtex/bib:4false.:/Library/Frameworks/R.framework/Resources/share/texmf/bibtex/bst::1.01/Library/Frameworks/R.framework/Resources/lib:/usr/local/jdk-21.jdk/Contents/Home/lib/servervi/Users/biocbuild/opt/homebrew/Cellar/opt/homebrew/opt/homebrew/opt/homebrew/share/info:/opt/homebrew/share/info:true/usr/local/jdk-21.jdk/Contents/Home22en_US.UTF-8Cen_GBln -sbiocbuild11.0make/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/share/man:/Library/Developer/CommandLineTools/usr/share/man:/Library/Developer/CommandLineTools/Toolchains/XcodeDefault.xctoolchain/usr/share/man:22/opt/R/arm64/lib/libssl.a /opt/R/arm64/lib/libcrypto.a/usr/bin/less/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/nGjcgFjVxO3au43UlFV3w/bin:/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/nGjcgFjVxO3au43UlFV3w/bin:/opt/homebrew/bin:/opt/homebrew/sbin:/Applications/CMake.app/Contents/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/usr/local/ncbi/igblast/bin:/usr/local/share/dotnet:/opt/salt:/opt/X11/bin:/Applications/quarto/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/Users/biocbuild/.cargo/bin:/opt/gfortran/bin:/opt/R/arm64/bin:/usr/local/lib/openbabel3/pkgconfig:/opt/R/arm64/lib/pkgconfig:/usr/local/lib/openbabel3/pkgconfig:/opt/R/arm64/lib/pkgconfig/Users/biocbuild/bbs-3.22-bioc/meat/SpectriPy/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/nGjcgFjVxO3au43UlFV3w/lib/python3.12/site-packages/rdkityesTRUE/usr/bin/open/usr/bin/bzip2/Library/Frameworks/R.framework/Resources/bin/Rcmd600/Library/Frameworks/R.framework/Resources/doc/Users/biocbuild/BBS/3.22/Renviron.bioc/usr/bin/gzip/Library/Frameworks/R.framework/Resources/Library/Frameworks/R.framework/Resources/includeSpectriPy/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-SpectriPy/00new/Library/Frameworks/R.framework/Resources/site-library/Users/biocbuild/Library/R/arm64/4.5/libraryunix/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-SpectriPy/00new/SpectriPySpectriPya4a4/usr/bin/openaarch64-apple-darwin20lpr/Library/Frameworks/R.framework/Resources/bin/qpdftimes,inconsolata,hyperPID=9545:NAME="reticulate"/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpKJ7Rqt/Library/Frameworks/R.framework/Resources/sharestrip -xstrip -S/opt/R/arm64/bin/texi2dvi/usr/bin/unzip4.5.1/usr/bin/zip/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/bin/sed/bin/bash6/tmp/ssh-bIwEKsfqDN/agent.21773155.52.47.40 59200 22155.52.47.40 59200 172.24.216.75 22/dev/ttys005/usr/bin/tarxterm-256color.:/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex:/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/biocbuild/Users/biocbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/nGjcgFjVxO3au43UlFV3wnGjcgFjVxO3au43UlFV3w20falsefalsepackage:_R_CHECK_PACKAGE_NAME_,abort,verbosepackage:_R_CHECK_PACKAGE_NAME_,abort,verbosetruetruetruetruetrueeqonlytruetrue0x1FA:0:0 Error: loading failed Execution halted ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/SpectriPy’