AndrewSkelton
commented
4 years ago Just to echo @ankushs0128 's observations, I'm seeing the same problem from upgrading to R v4.
Seems like this issue is also seen in #87 and presto
Open ankushs0128 opened 4 years ago
AndrewSkelton
commented
4 years ago Just to echo @ankushs0128 's observations, I'm seeing the same problem from upgrading to R v4.
Seems like this issue is also seen in #87 and presto
slowkow
commented
4 years ago I just tried installing presto and harmony on R 4.0.2 on Linux, and it worked just fine:
devtools::install_github("immunogenomics/presto")See the full log here for presto: https://github.com/immunogenomics/presto/issues/8#issuecomment-653934011
devtools::install_github("immunogenomics/harmony")Here's the log for harmony:
> devtools::install_github("immunogenomics/harmony")
Downloading GitHub repo immunogenomics/harmony@master
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: processx (3.4.2 -> 3.4.3) [CRAN]
Enter one or more numbers, or an empty line to skip updates:
2
SingleCel... (NA -> 1.10.1) [CRAN]
processx (3.4.2 -> 3.4.3 ) [CRAN]
Installing 2 packages: SingleCellExperiment, processx
Installing packages into ‘/home/ks38/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://bioconductor.org/packages/3.11/bioc/src/contrib/SingleCellExperiment_1.10.1.tar.gz'
Content type 'application/x-gzip' length 620347 bytes (605 KB)
==================================================
downloaded 605 KB
trying URL 'https://cran.rstudio.com/src/contrib/processx_3.4.3.tar.gz'
Content type 'application/x-gzip' length 132841 bytes (129 KB)
==================================================
downloaded 129 KB
* installing *source* package ‘SingleCellExperiment’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SingleCellExperiment)
* installing *source* package ‘processx’ ...
** package ‘processx’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall tools/px.c -o tools/px
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g supervisor/supervisor.c supervisor/utils.c \
-o supervisor/supervisor
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c client.c -o client.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c errors.c -o errors.o
gcc -std=gnu99 -shared -L"/usr/lib/R/lib" -Wl,-Bsymbolic-functions -Wl,-z,relro -o client.so base64.o client.o errors.o -L"/usr/lib/R/lib" -lR
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c poll.c -o poll.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c processx-connection.c -o processx-connection.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c processx-vector.c -o processx-vector.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c create-time.c -o create-time.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/childlist.c -o unix/childlist.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/connection.c -o unix/connection.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/processx.c -o unix/processx.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/sigchld.c -o unix/sigchld.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/utils.c -o unix/utils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/named_pipe.c -o unix/named_pipe.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cleancall.c -o cleancall.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o processx.so init.o poll.o errors.o processx-connection.o processx-vector.o create-time.o base64.o unix/childlist.o unix/connection.o unix/processx.o unix/sigchld.o unix/utils.o unix/named_pipe.o cleancall.o -L/usr/lib/R/lib -lR
installing via 'install.libs.R' to /home/ks38/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-processx/00new/processx
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (processx)
The downloaded source packages are in
‘/tmp/Rtmpmw4rJy/downloaded_packages’
✔ checking for file ‘/tmp/Rtmpmw4rJy/remotesf8fb488142c5/immunogenomics-harmony-88b1e2a/DESCRIPTION’ ...
─ preparing ‘harmony’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘harmony_1.0.tar.gz’
Installing package into ‘/home/ks38/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
* installing *source* package ‘harmony’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppProgress/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-ttHamR/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c harmony.cpp -o harmony.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o harmony.so RcppExports.o harmony.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/ks38/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-harmony/00new/harmony/libs
** R
** data
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (harmony)
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] ps_1.3.3 fansi_0.4.1 prettyunits_1.1.1 rprojroot_1.3-2
[5] withr_2.2.0 digest_0.6.25 crayon_1.3.4 assertthat_0.2.1
[9] R6_2.4.1 backports_1.1.8 magrittr_1.5 rlang_0.4.6
[13] cli_2.0.2 curl_4.3 fs_1.4.2 remotes_2.1.1
[17] testthat_2.3.2 callr_3.4.3 ellipsis_0.3.1 desc_1.2.0
[21] devtools_2.3.0 tools_4.0.2 glue_1.4.1 pkgload_1.1.0
[25] compiler_4.0.2 processx_3.4.2 pkgbuild_1.0.8 sessioninfo_1.1.1
[29] memoise_1.1.0 usethis_1.6.1
clarsenEmory
commented
4 years ago slowkow, I have updated from 4.0 to 4.02. I can install harmony now. I will test it to make sure it runs in our pipelines. Thank you
AndrewSkelton
commented
4 years ago I'm having the same issue coming through (and seen in #87 ), after upgrading to R 4.0.2. This error also still persists in presto. Full log below, and I tried checking the temp file that is referred to but can't seem to capture it (destroyed). I've looked through Source and can't see any red flags, especially if it's passing Travis tests.
I ran an Ubuntu docker container and installed a fresh version of R, devtools, and Harmony which worked as an alternative, but far from ideal. Happy to dig into any suggestions, but can't seem to capture the point at which the installation is breaking.
> devtools::install_github("immunogenomics/harmony")
Downloading GitHub repo immunogenomics/harmony@master
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: processx (3.4.2 -> 3.4.3) [CRAN]
Enter one or more numbers, or an empty line to skip updates:
1
processx (3.4.2 -> 3.4.3) [CRAN]
Installing 1 packages: processx
There is a binary version available but the source version is later:
binary source needs_compilation
processx 3.4.2 3.4.3 TRUE
Do you want to install from sources the package which needs compilation? (Yes/no/cancel) no
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.0/processx_3.4.2.tgz'
Content type 'application/x-gzip' length 252447 bytes (246 KB)
==================================================
downloaded 246 KB
The downloaded binary packages are in
/var/folders/dl/yg3x4x1s75bbf9ph3yd4jrbr0000gn/T//Rtmp9EaCy3/downloaded_packages
✓ checking for file ‘/private/var/folders/dl/yg3x4x1s75bbf9ph3yd4jrbr0000gn/T/Rtmp9EaCy3/remotes919b6b2feb38/immunogenomics-harmony-88b1e2a/DESCRIPTION’ ...
─ preparing ‘harmony’:
✓ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘harmony_1.0.tar.gz’
* installing *source* package ‘harmony’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I/usr/local/include -fPIC -Wall -g -O2 -c harmony.cpp -o harmony.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o harmony.so RcppExports.o harmony.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-harmony/00new/harmony/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
sh: line 1: 37528 Killed: 9 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/dl/yg3x4x1s75bbf9ph3yd4jrbr0000gn/T//Rtmpjo4yGw/file927f1b3ed486'
ERROR: installing package indices failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/harmony’
Error: Failed to install 'harmony' from GitHub:
(converted from warning) installation of package ‘/var/folders/dl/yg3x4x1s75bbf9ph3yd4jrbr0000gn/T//Rtmp9EaCy3/file919baac57b3/harmony_1.0.tar.gz’ had non-zero exit status
> devtools::install_github("immunogenomics/presto")
Downloading GitHub repo immunogenomics/presto@master
Skipping 1 packages not available: DESeq2
✓ checking for file ‘/private/var/folders/dl/yg3x4x1s75bbf9ph3yd4jrbr0000gn/T/Rtmp9EaCy3/remotes919b7ae03632/immunogenomics-presto-7f63f96/DESCRIPTION’ ...
─ preparing ‘presto’:
✓ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘presto_1.0.0.tar.gz’
* installing *source* package ‘presto’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fast_wilcox.cpp -o fast_wilcox.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o presto.so RcppExports.o fast_wilcox.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-presto/00new/presto/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
sh: line 1: 37620 Killed: 9 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/dl/yg3x4x1s75bbf9ph3yd4jrbr0000gn/T//RtmpH4fsOF/file92de2d299c2b'
ERROR: installing package indices failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/presto’
Error: Failed to install 'presto' from GitHub:
(converted from warning) installation of package ‘/var/folders/dl/yg3x4x1s75bbf9ph3yd4jrbr0000gn/T//Rtmp9EaCy3/file919b16064ba4/presto_1.0.0.tar.gz’ had non-zero exit statusSession Info
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] forcats_0.5.0 stringr_1.4.0 dplyr_1.0.0 purrr_0.3.4 readr_1.3.1 tidyr_1.1.0 tibble_3.0.1 ggplot2_3.3.2 tidyverse_1.3.0
loaded via a namespace (and not attached):
[1] httr_1.4.1 pkgload_1.1.0 jsonlite_1.7.0 modelr_0.1.8 assertthat_0.2.1 blob_1.2.1 cellranger_1.1.0 yaml_2.2.1 remotes_2.1.1
[10] sessioninfo_1.1.1 pillar_1.4.4 backports_1.1.8 lattice_0.20-41 glue_1.4.1 digest_0.6.25 rvest_0.3.5 colorspace_1.4-1 htmltools_0.5.0
[19] plyr_1.8.6 pkgconfig_2.0.3 devtools_2.3.0 broom_0.5.6 haven_2.3.1 scales_1.1.1 processx_3.4.2 generics_0.0.2 usethis_1.6.1
[28] ellipsis_0.3.1 withr_2.2.0 cli_2.0.2 magrittr_1.5 crayon_1.3.4 readxl_1.3.1 memoise_1.1.0 evaluate_0.14 ps_1.3.3
[37] fs_1.4.1 fansi_0.4.1 nlme_3.1-148 xml2_1.3.2 pkgbuild_1.0.8 tools_4.0.2 prettyunits_1.1.1 hms_0.5.3 lifecycle_0.2.0
[46] munsell_0.5.0 reprex_0.3.0 callr_3.4.3 compiler_4.0.2 tinytex_0.24 rlang_0.4.6 grid_4.0.2 rstudioapi_0.11 rmarkdown_2.3
[55] testthat_2.3.2 gtable_0.3.0 DBI_1.1.0 curl_4.3 reshape2_1.4.4 R6_2.4.1 lubridate_1.7.9 knitr_1.29 rprojroot_1.3-2
[64] desc_1.2.0 stringi_1.4.6 Rcpp_1.0.4.6 vctrs_0.3.1 dbplyr_1.4.4 tidyselect_1.1.0 xfun_0.15 @AndrewSkelton
Please let me know whether you are able to install these other packages on your macOS system. I still don't have a clear ideas about what is going wrong, but comparing and contrasting different packages that work or do not work might help to narrow down the possibilities. I am starting to suspect that it is something particular about your system (e.g. the C++ compiler).
devtools::install_github("tidyverse/glue")
devtools::install_github("slowkow/ggrepel")@slowkow - Thanks for the questions. Hope this helps narrow the issues:
glue and ggrepel install without issue and libraries load without issuedevtools::install_github("jl354/bcSeq"))So I'm a bit stumped as to what's causing this.
ankushs0128
commented
4 years ago I did updated R 4.0,0 to R 4.0.2 and
devtools::install_github("immunogenomics/presto")
devtools::install_github("immunogenomics/harmony")
it still shows the similar error
> ##installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-presto/00new/presto/libs
> ** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
> sh: line 1: 59022 Killed: 9 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/st/7_q6h2897zv73w3x6g85m6y80000gn/T//Rtmpg2JU72/filee66b75c49e26'
> ERROR: installing package indices failed
> * removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/presto’
> Error: Failed to install 'presto' from GitHub:
> (converted from warning) installation of package
> ‘/var/folders/st/7_q6h2897zv73w3x6g85m6y80000gn/T//RtmpuFb2VP/file849d4590f431/presto_1.0.0.tar.gz’` had non-zero exit statusHowever
devtools::install_github("tidyverse/glue") installs just fine.
Any pointers to Install rectify the error !!
slowkow
commented
4 years ago @clarsenEmory @petervangalen @newuser0101 @13mhzeng @ilonliu @RMolania @ankushs0128
Please consider sharing more information.
By sharing the complete output for the sessionInfo() command in R, we will learn:
Please also share:
Here is the information I have gleaned from messages so far:
ankushs0128
commented
4 years ago Here is the session info
sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] clustree_0.4.3 ggraph_2.0.3 Rsamtools_2.4.0
[4] ggrepel_0.8.2 gtable_0.3.0 uwot_0.1.8
[7] ggridges_0.5.2 gridExtra_2.3 nabor_0.5.0
[10] Seurat_3.1.5 progress_1.2.2 TxDb.Hsapiens.UCSC.hg38.knownGene_3.10.0
[13] GenomicFeatures_1.40.0 org.Hs.eg.db_3.11.4 AnnotationDbi_1.50.1
[16] BSgenome.Hsapiens.UCSC.hg38_1.4.3 BSgenome_1.56.0 rtracklayer_1.48.0
[19] Biostrings_2.56.0 XVector_0.28.0 ArchR_0.9.5
[22] magrittr_1.5 rhdf5_2.32.2 Matrix_1.2-18
[25] data.table_1.12.8 SummarizedExperiment_1.18.1 DelayedArray_0.14.0
[28] matrixStats_0.56.0 Biobase_2.48.0 GenomicRanges_1.40.0
[31] GenomeInfoDb_1.24.2 IRanges_2.22.2 S4Vectors_0.26.1
[34] BiocGenerics_0.34.0 ggplot2_3.3.2
loaded via a namespace (and not attached):
[1] reticulate_1.16 R.utils_2.9.2 tidyselect_1.1.0 RSQLite_2.2.0
[5] htmlwidgets_1.5.1 BiocParallel_1.22.0 Rtsne_0.15 devtools_2.3.0
[9] DropletUtils_1.8.0 munsell_0.5.0 codetools_0.2-16 ica_1.0-2
[13] future_1.17.0 withr_2.2.0 colorspace_1.4-1 knitr_1.29
[17] rstudioapi_0.11 SingleCellExperiment_1.10.1 ROCR_1.0-11 listenv_0.8.0
[21] labeling_0.3 GenomeInfoDbData_1.2.3 polyclip_1.10-0 farver_2.0.3
[25] bit64_0.9-7 rprojroot_1.3-2 vctrs_0.3.1 generics_0.0.2
[29] xfun_0.15 BiocFileCache_1.12.0 R6_2.4.1 graphlayouts_0.7.0
[33] rsvd_1.0.3 locfit_1.5-9.4 bitops_1.0-6 assertthat_0.2.1
[37] scales_1.1.1 babelwhale_1.0.1 Cairo_1.5-12 globals_0.12.5
[41] processx_3.4.3 tidygraph_1.2.0 rlang_0.4.6 splines_4.0.2
[45] lazyeval_0.2.2 hexbin_1.28.1 BiocManager_1.30.10 yaml_2.2.1
[49] reshape2_1.4.4 backports_1.1.8 tools_4.0.2 usethis_1.6.1
[53] ellipsis_0.3.1 RColorBrewer_1.1-2 sessioninfo_1.1.1 Rcpp_1.0.5
[57] plyr_1.8.6 zlibbioc_1.34.0 purrr_0.3.4 RCurl_1.98-1.2
[61] ps_1.3.3 prettyunits_1.1.1 openssl_1.4.2 viridis_0.5.1
[65] pbapply_1.4-2 cowplot_1.0.0 dynparam_1.0.1 zoo_1.8-8
[69] cluster_2.1.0 fs_1.4.2 RSpectra_0.16-0 carrier_0.1.0
[73] lmtest_0.9-37 RANN_2.6.1 fitdistrplus_1.1-1 pkgload_1.1.0
[77] hms_0.5.3 patchwork_1.0.1 XML_3.99-0.4 testthat_2.3.2
[81] compiler_4.0.2 biomaRt_2.44.1 tibble_3.0.1 KernSmooth_2.23-17
[85] crayon_1.3.4 R.oo_1.23.0 htmltools_0.5.0 proxyC_0.1.5
[89] tidyr_1.1.0 RcppParallel_5.0.2 DBI_1.1.0 tweenr_1.0.1
[93] dbplyr_1.4.4 MASS_7.3-51.6 rappdirs_0.3.1 readr_1.3.1
[97] cli_2.0.2 R.methodsS3_1.8.0 igraph_1.2.5 pkgconfig_2.0.3
[101] GenomicAlignments_1.24.0 plotly_4.9.2.1 dqrng_0.2.1 dynutils_1.0.5
[105] stringr_1.4.0 callr_3.4.3 digest_0.6.25 sctransform_0.2.1
[109] RcppAnnoy_0.0.16 tsne_0.1-3 leiden_0.3.3 edgeR_3.30.3
[113] curl_4.3 gtools_3.8.2 lifecycle_0.2.0 nlme_3.1-148
[117] jsonlite_1.7.0 Rhdf5lib_1.10.0 dynwrap_1.2.1 desc_1.2.0
[121] viridisLite_0.3.0 askpass_1.1 limma_3.44.3 fansi_0.4.1
[125] pillar_1.4.4 lattice_0.20-41 httr_1.4.1 pkgbuild_1.0.8
[129] survival_3.2-3 glue_1.4.1.9000 remotes_2.1.1 png_0.1-7
[133] bit_1.1-15.2 ggforce_0.3.2 stringi_1.4.6 HDF5Array_1.16.1
[137] blob_1.2.1 memoise_1.1.0 dplyr_1.0.0 irlba_2.3.3
[141] future.apply_1.6.0 ape_5.4 The harmony package installs without issues on:
My best guesses:
gfortran?I noticed that GitHub Actions uses a different version of macOS (10.15), so I may try to set that up and see what the result will be.
slowkow
commented
4 years ago I used GitHub Actions and found that harmony installs without issues on:
Here, you can view the results for five different combinations of OS and R versions:
For those of you experiencing issues, I wonder if you have used Homebrew to install gfortran or other compilation tools?
Please consider sharing the following:
readlink -f $(which gfortran)readlink -f $(which clang++)cat ~/.R/MakevarsAndrewSkelton
commented
4 years ago That did the trick - seems that my system had gfortran installed via brew. Removing the brew version, and installing the gfortran binaries from r-project tools, and adding that to the path did the trick. Thanks for the assistance!
slowkow
commented
4 years ago Hooray! Thank you for letting us know, Andrew! Sorry for the long and tedious journey.
I hope that this solves the issue for everyone.
By the way, I'm not confident that you need to download and install the gfortran binaries if you are using CRAN R 4.0.0 builds and higher. I don't recall how I got gfortran on my Mac, but I know that I had to install Xcode with xcode-select --install.
This is what I see on the R-Project website: https://cran.r-project.org/bin/macosx/tools/
R for Mac OS X
Development Tools and Libraries
CRAN R 4.0.0 builds and higher no longer use any custom compilers and thus this directory is no longer relevant. We now use Apple Xcode 10.1 and GNU Fortran 8.2 from https://github.com/fxcoudert/gfortran-for-macOS/releases. For more details on compiling R, please see also https://mac.R-project.org/tools/
These instructions might also be helpful: https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/
ankushs0128
commented
4 years ago No luck !! It´s still showing the same error.
Removed and reinstalled R Compiler Tools for Rcpp on OS X
GNU Fortran (GCC) 8.2.0
Reinstalled Xcode!
However, I tried on another macOS, it installed without a problem. But couldn´t figure out the problem.
slowkow
commented
4 years ago @ankushs0128 Thank you for reporting that the installation works on another macOS system. That helps us to confirm that the issue is not with harmony code, but instead with system settings.
I inspected the commands run by GitHub Actions and this is what I found for installing R on macOS:
brew cask install gfortran
brew install qpdf pkgconfig checkbashisms
sudo installer -pkg /Users/runner/work/_temp/R-4.0.2.pkg -target /
For additional assistance, you might consider creating a post on RStudio Community. The folks at RStudio have a lot of expertise in setting up R. Please consider sharing with them all of your relevant system details (entire command, entire output, sessionInfo() output, gfortran version, clang++ version, macOS version, R version, Xcode version, contents of ~/.Renviron ~/.Rprofile ~/.R/Makevars, etc.).
Without additional information from you, this is the best I can do. Good luck!
ankushs0128
commented
4 years ago Thanks, @slowkow !! I guess something was messed up with the clang++ version. The error resolved after I removed all clang versions (version [11)] (https://thecoatlessprofessor.com/programming/r/uninstalling-the-r-development-toolchain-on-macos/) from the system
I reinstalled Xcode, R 4.0.2 and then gfortran as suggested by @slowkow
brew cask install gfortran brew install qpdf pkgconfig checkbashisms
Note , There are no ~/.R/Makevars files in R 4.0.2 (at least) in my system !
Installing harmony in R (4.0.0 on MacOS) directly from Github is giving an error message :-
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-harmony/00new/harmony/libs` `** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices` `sh: line 1: 41345 Killed: 9 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/st/7_q6h2897zv73w3x6g85m6y80000gn/T//RtmpV8yJrp/filea158311e5ff1' ERROR: installing package indices failed` `* removing `‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/harmony’` `Error:` Failed to install 'harmony' from GitHub: (converted from warning) installation of package '/var/folders/st/7_q6h2897zv73w3x6g85m6y80000gn/T//RtmpvaXZe9/file39e50bbbee8/harmony_1.0.tar.gz' had non-zero exit statusAny pointer to rectify the error
MRogne007
commented
4 years ago Hi all,
I'm also trying to use Harmony and I´m also facing same problems, I tried all the above listed steps for installation, but to no success. Any suggestion to circumvent the problem.
> installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-harmony/00new/harmony/libs
> ** R
> ** data
> ** byte-compile and prepare package for lazy loading
> ** help
> *** installing help indices
> *** copying figures
> ** building package indices
> sh: line 1: 11135 Killed: 9 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/_w/dxrw0fl57zgb9h88m5d39fcw0000gn/T//RtmprrRk3v/file2b61322b1d86'
> ERROR: installing package indices failed
> * removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/harmony’
> Error: Failed to install 'harmony' from GitHub:
> (converted from warning) installation of package ‘/var/folders/_w/dxrw0fl57zgb9h88m5d39fcw0000gn/T//RtmpiNfEjt/file20ce209f03fe/harmony_1.0.tar.gz’ had non-zero exit status Session info ────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.0.2 (2020-06-22)
os macOS Catalina 10.15.5
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Oslo
date 2020-07-10
─ Packages ────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
backports 1.1.8 2020-06-17 [1] CRAN (R 4.0.0)
BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.0)
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.0)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
devtools * 2.3.0 2020-04-10 [1] CRAN (R 4.0.0)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
fs 1.4.2 2020-06-30 [1] CRAN (R 4.0.0)
glue 1.4.1 2020-05-13 [1] CRAN (R 4.0.0)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.2)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
Matrix * 1.2-18 2019-11-27 [1] CRAN (R 4.0.2)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
pkgbuild 1.0.8 2020-05-07 [1] CRAN (R 4.0.0)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.0)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0)
processx 3.4.3 2020-07-05 [1] CRAN (R 4.0.0)
ps 1.3.3 2020-05-08 [1] CRAN (R 4.0.0)
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0)
rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.0)
usethis * 1.6.1 2020-04-29 [1] CRAN (R 4.0.0)
withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0)
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library@MRogne007 Did you follow the instructions here?
https://thecoatlessprofessor.com/programming/r/uninstalling-the-r-development-toolchain-on-macos/
MRogne007
commented
4 years ago yes i did
slowkow
commented
4 years ago @MRogne007 Please consider sharing more information:
cat ~/.R/Makevars
cat ~/.Renviron
readlink -f $(which gfortran)
readlink -f $(which clang++)
ls -lah /usr/local/clang*
ls -lah /usr/local/gfortran*
ls -lah /usr/local/bin/gfortran*
ls -lah /private/var/db/receipts/com.gnu.gfortran*
ls -lah /private/var/db/receipts/com.rbinaries.clang*How did you install R? (brew, download .pkg file from r-project.org, etc.)
slowkow
commented
4 years ago @MRogne007 What happens if you try this?
mv ~/.miniconda3{,.bak} # temporarily move the miniconda folder to disable it
R -e 'devtools::install_github("immunogenomics/harmony")
ilonliu
commented
4 years ago @slowkow
I have been trying around with all different approaches mentioned above, including re-installing the toolchain and gfortran, which all didn't work. However, what worked now on my macOS Mojave 10.14.6 R version 4.0.2 is:
git clone https://github.com/immunogenomics/harmonydevtools::install_local("harmony")This solved the problem. I have already run Harmony on some data and it seems to work well. Not sure of course whether any other features may be affected by this approach, so happy about your feedback there. Thanks!
slowkow
commented
4 years ago Hi @ilonliu, thanks for the report. The data files are not essential. If they are causing installation issues, we should certainly modify them or simply remove them.
I know this might be a stretch, but would it be possible for you to share the commands and error messages that you saw? And then the same commands and messages after deleting the data files? This would help me to understand the issue.
ilonliu
commented
4 years ago Original error with devtools::install_github("immunogenomics/harmony"):
Downloading GitHub repo immunogenomics/harmony@HEAD
✓ checking for file ‘/private/var/folders/gw/fht9stfj07xgnyfjcd5lj3g1zjt397/T/RtmpqWK0xP/remotesc50020ce03a4/immunogenomics-harmony-88b1e2a/DESCRIPTION’ ...
─ preparing ‘harmony’:
✓ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘harmony_1.0.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'
* installing *source* package ‘harmony’ ...
** using staged installation
** libs
/usr/local/clang4/bin/clang++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
/usr/local/clang4/bin/clang++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I/usr/local/include -fPIC -Wall -g -O2 -c harmony.cpp -o harmony.o
/usr/local/clang4/bin/clang++ -fopenmp -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang4/lib -o harmony.so RcppExports.o harmony.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-harmony/00new/harmony/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
sh: line 1: 50565 Killed: 9 R_TESTS= '/Library/Frameworks/R.framework/Resources/bin/R' --no-save --no-restore --no-echo 2>&1 < '/var/folders/gw/fht9stfj07xgnyfjcd5lj3g1zjt397/T//RtmpriywuW/filec56a7d3ada46'
ERROR: installing package indices failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/harmony’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/harmony’
installation of package ‘/var/folders/gw/fht9stfj07xgnyfjcd5lj3g1zjt397/T//RtmpqWK0xP/filec5006c18db94/harmony_1.0.tar.gz’ had non-zero exit statusAfter cloning the repository and deleting the data files, running devtools::install_local("harmony"):
✓ checking for file ‘/private/var/folders/gw/fht9stfj07xgnyfjcd5lj3g1zjt397/T/RtmpqWK0xP/filec500d283149/harmony/DESCRIPTION’ ...
─ preparing ‘harmony’:
✓ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘harmony_1.0.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'
* installing *source* package ‘harmony’ ...
** using staged installation
** libs
/usr/local/clang4/bin/clang++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
/usr/local/clang4/bin/clang++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppProgress/include' -I/usr/local/include -fPIC -Wall -g -O2 -c harmony.cpp -o harmony.o
/usr/local/clang4/bin/clang++ -fopenmp -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang4/lib -o harmony.so RcppExports.o harmony.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-harmony/00new/harmony/libs
** R
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (harmony)sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] harmony_1.0 Rcpp_1.0.5 devtools_2.3.1 usethis_1.6.1
loaded via a namespace (and not attached):
[1] pillar_1.4.6 compiler_4.0.2 BiocManager_1.30.10
[4] prettyunits_1.1.1 remotes_2.2.0 tools_4.0.2
[7] testthat_2.3.2 digest_0.6.25 pkgbuild_1.1.0
[10] pkgload_1.1.0 tibble_3.0.3 lifecycle_0.2.0
[13] gtable_0.3.0 evaluate_0.14 memoise_1.1.0
[16] pkgconfig_2.0.3 rlang_0.4.7 cli_2.0.2
[19] rstudioapi_0.11 curl_4.3 yaml_2.2.1
[22] xfun_0.16 dplyr_1.0.2 withr_2.2.0
[25] knitr_1.29 generics_0.0.2 vctrs_0.3.3
[28] desc_1.2.0 fs_1.5.0 tidyselect_1.1.0
[31] grid_4.0.2 cowplot_1.0.0 rprojroot_1.3-2
[34] glue_1.4.2 R6_2.4.1 processx_3.4.3
[37] fansi_0.4.1 rmarkdown_2.3 sessioninfo_1.1.1
[40] purrr_0.3.4 ggplot2_3.3.2 callr_3.4.3
[43] magrittr_1.5 codetools_0.2-16 scales_1.1.1
[46] backports_1.1.9 ps_1.3.4 ellipsis_0.3.1
[49] htmltools_0.5.0 assertthat_0.2.1 colorspace_1.4-1
[52] munsell_0.5.0 crayon_1.3.4 @ilonliu Thank you so much!
Here's my guess about what might be happening. I guess that the data files might be dependent on some versions of multiple R packages, and those packages are not specified in DESCRIPTION or elsewhere. Then, users who lack those packages (or have different versions) cannot load the data files. That's my best guess. I would have to try to inspect the files to learn more. I may be wrong.
@ilyakorsunsky I think we need to double-check what is going on with those data files — it seems they may be causing installation issues for some users. I think the safest thing to do is to delete them. Then, the next safest option would be to delete them and re-create new files scratch, but this time ensure that the objects saved in the .rda files have zero dependencies on other R packages. Alternatively, we can make sure that all of the object's R package dependencies are explicitly listed in DESCRIPTION.
It's concerning that the Travis and Appveyor installations seem to work, and yet some users still have installation issues. This issue serves as a reminder that Travis and Appveyor tests are necessary, but not sufficient.
Meggie-MH
commented
4 years ago 3. devtools::install_local("harmony")
deleting data folder works for me. Thank you!
coffeeCowLu
commented
4 years ago i finished it:
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
library(harmony)
packageVersion('harmony')
[1] ‘1.0’by:
wget https://github.com/immunogenomics/harmony/archive/master.zip # or download by webpagelibrary(devtools)
install_local('yourpath/harmony-master.zip')good luck to you !!!
joonan30
commented
3 years ago I feel I ought to report. Mine is R 3.6.1.
Thanks for the great tool.
kelsi-kw
commented
3 years ago MacOS: BigSur version 11.0.1
platform x86_64-apple-darwin17.0
version.string R version 4.0.3 (2020-10-10)
nickname Bunny-Wunnies Freak Out
I was having similar issues to users above. Just thought I would add this in case it would work for anyone else. I downloaded https://github.com/immunogenomics/harmony/archive/master.zip and added a line to the DESCRIPTION file "SystemRequirements: C++11". Then it installed. Thanks for this tool!
vsuryaw
commented
3 years ago MacOS: BigSur version 11.0.1 platform x86_64-apple-darwin17.0 version.string R version 4.0.3 (2020-10-10) nickname Bunny-Wunnies Freak Out
I was having similar issues to users above. Just thought I would add this in case it would work for anyone else. I downloaded https://github.com/immunogenomics/harmony/archive/master.zip and added a line to the DESCRIPTION file "SystemRequirements: C++11". Then it installed. Thanks for this tool!
Thanks Kelsi-kw , this is the only one that worked for me! on MacOS: Catalina version 10.15.7, platform x86_64-apple-darwin17.0, version.string R version 4.0.4 (2021-02-15)
Installing harmony in R (4.0.0 on MacOS) directly from Github is giving an error message :-
Any pointer to rectify the error