Error installing Harmony on R version 4.0.0 (2020-04-24)

[ankushs0128]

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 status

Any pointer to rectify the error

[AndrewSkelton]

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]

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: immunogenomics/presto#8 (comment)

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]

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]

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 status

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_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 

[slowkow]

@AndrewSkelton

• Is it true that you are not seeing issues on Ubuntu but you are seeing this issue on macOS 10.15.4?
• Are you able to install any other GitHub R packages on your macOS system? Do these packages use Rcpp?
• How did you install R on macOS? Did you use homebrew? Did you download R-4.0.2.pkg (I always do this, I had problems with homebrew)? Something else?

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")

[AndrewSkelton]

@slowkow - Thanks for the questions. Hope this helps narrow the issues:

• Both glue and ggrepel install without issue and libraries load without issue
• Correct - No issue on Ubuntu, but issue is on the macOS system.
• I've installed a number of other github R packages successfully
  • I've installed bcSeq which has some underlying Rcpp methods I believe (devtools::install_github("jl354/bcSeq"))
  • If there are any other packages you can suggest that have a similar implementation of Rcpp to Harmony or presto then I'll happily try and install them.
• R is installed using the pkg file from the r-project website, not homebrew

So I'm a bit stumped as to what's causing this.

[ankushs0128]

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  status

However
devtools::install_github("tidyverse/glue") installs just fine.

Any pointers to Install rectify the error !!

[slowkow]

@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:

• What operating system are you using? macOS, Windows, Linux, etc.
• What R version are you using? 3.6.2, 4.0.0, etc.

Please also share:

• How did you install R? Homebrew? The .pkg file from r-project.org? Something else?

Here is the information I have gleaned from messages so far:

[ankushs0128]

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 

[slowkow]

The harmony package installs without issues on:

• macOS High Sierra 10.13.6
• Ubuntu 16.04.6 LTS
• Windows Server 2012 R2 x64 (build 9600)

My best guesses:

• Maybe something changed in newer versions of macOS?
• Maybe something is not working with compilation tools like 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]

I used GitHub Actions and found that harmony installs without issues on:

• macOS 10.15.5

Here, you can view the results for five different combinations of OS and R versions:

• https://github.com/slowkow/harmony/runs/846868505?check_suite_focus=true

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/Makevars

[AndrewSkelton]

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]

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]

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]

@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]

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 status

Any pointer to rectify the error

[MRogne007]

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

[slowkow]

@MRogne007 Did you follow the instructions here?

https://thecoatlessprofessor.com/programming/r/uninstalling-the-r-development-toolchain-on-macos/

[MRogne007]

yes i did

[slowkow]

@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]

@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]

@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:

1. cloned harmony into my working directory: git clone https://github.com/immunogenomics/harmony
2. I deleted the /harmony/data folder, which contained several cell_lines*.RData files and I believe are not essential? Please correct me if I'm wrong. I tried this after reading: https://r.789695.n4.nabble.com/quot-ERROR-installing-package-indices-failed-quot-message-when-building-my-package-td4687321.html, where it seemed files in the /data folder were blocking the index build
3. I installed harmony locally in R: devtools::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]

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]

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 status

After 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  

[slowkow]

@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]

3. devtools::install_local("harmony")

deleting data folder works for me. Thank you!

[coffeeCowLu]

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 webpage

library(devtools)
install_local('yourpath/harmony-master.zip')

good luck to you !!!

[joonan30]

I feel I ought to report. Mine is R 3.6.1.

1. Got the error from dev install. (I thought my cpp or gfortlan are correctly installed)
2. Downloaded the source file and unzip.
3. install.packages('harmony-master/', repos = NULL, type = "source") and it works.

Thanks for the great tool.

[kelsi-kw]

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]

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)