dyplr error in q2-Breakaway

Hi @Amy_Willis and possibly others,

I’m having an issue with q2-breakaway in QIIME 2019.10.0. Specifically, Im getting errors with dyplr (see below). Im not sure if this is a complier problem, or something in conflict since hte last breakaway version I can find was for 2018.8. Any advice would be appreciated.

Best,
Justine

Verbose output below:

Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: run_new_richness.R /var/folders/bw/q064ds0d2795_6mxnrssf0l1gkw0rj/T/tmp79usq_in/table.tsv /var/folders/bw/q064ds0d2795_6mxnrssf0l1gkw0rj/T/q2-AlphaDiversityFormat-ne3fy66f

R version 3.5.1 (2018-07-02) 
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ade4 ape askpass assertthat backports base BH Biobase BiocGenerics BiocParallel biomformat Biostrings bitops brew callr cli clipr clisymbols cluster codetools colorspace commonmark compiler covr crayon crosstalk curl dada2 data.table datasets DelayedArray desc devtools digest dplyr DT ellipsis evaluate fansi farver foreach formatR fs futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 gh git2r glue graphics grDevices grid gtable htmltools htmlwidgets httr hwriter igraph ini IRanges isoband iterators jsonlite labeling lambda.r later lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix matrixStats memoise methods mgcv mime multtest munsell nlme openssl parallel permute phyloseq pillar pixmap pkgbuild pkgconfig pkgload plogr plyr praise prettyunits processx promises ps purrr R.cache R.methodsS3 R.oo R.utils R6 rcmdcheck RColorBrewer Rcpp RcppParallel RCurl remotes reshape2 rex rhdf5 Rhdf5lib rlang roxygen2 rprojroot Rsamtools rstudioapi rversions S4Vectors scales sessioninfo ShortRead snow sp splines stats stats4 stringi stringr SummarizedExperiment survival sys tcltk testthat tibble tidyselect tools usethis utf8 utils vctrs vegan viridisLite whisker withr xml2 xopen XVector yaml zeallot zlibbiocYou have tibble installed!

You have magrittr installed!

Thank god! devtools is already available

Great! phyloseq is already available

Attempting to make phyloseq object...

[1] "otu_table"
attr(,"package")
[1] "phyloseq"
Downloading GitHub repo adw96/[email protected]
dplyr   (0.8.3 -> 0.8.5 ) [CRAN]
ggplot2 (3.2.1 -> 3.3.0 ) [CRAN]
R.rsp   (NA    -> 0.43.2) [CRAN]
Skipping 1 packages not available: phyloseq
Installing 3 packages: dplyr, ggplot2, R.rsp
trying URL 'https://cloud.r-project.org/src/contrib/dplyr_0.8.5.tar.gz'
Content type 'application/x-gzip' length 1378766 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cloud.r-project.org/src/contrib/ggplot2_3.3.0.tar.gz'
Content type 'application/x-gzip' length 3031461 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

trying URL 'https://cloud.r-project.org/src/contrib/R.rsp_0.43.2.tar.gz'
Content type 'application/x-gzip' length 839242 bytes (819 KB)
==================================================
downloaded 819 KB

* installing *source* package ‘dplyr’ ...
** package ‘dplyr’ successfully unpacked and MD5 sums checked
** libs
x86_64-apple-darwin13.4.0-clang++  -I"/Users/jusdeb/miniconda3/envs/micc/lib/R/include" -DNDEBUG -I../inst/include -DRCPP_DEFAULT_INCLUDE_CALL=false -DCOMPILING_DPLYR -DRCPP_USING_UTF8_ERROR_STRING -DRCPP_USE_UNWIND_PROTECT -DBOOST_NO_AUTO_PTR  -I"/Users/jusdeb/miniconda3/envs/micc/lib/R/library/BH/include" -I"/Users/jusdeb/miniconda3/envs/micc/lib/R/library/plogr/include" -I"/Users/jusdeb/miniconda3/envs/micc/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/jusdeb/miniconda3/envs/micc/include   -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/Users/jusdeb/miniconda3/envs/micc/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/dplyr.h:4:
In file included from ../inst/include/dplyr/main.h:6:
In file included from ../inst/include/dplyr/workarounds/static_assert.h:17:
In file included from /Users/jusdeb/miniconda3/envs/micc/lib/R/library/BH/include/boost/config.hpp:57:
In file included from /Users/jusdeb/miniconda3/envs/micc/lib/R/library/BH/include/boost/config/platform/macos.hpp:28:
In file included from /Users/jusdeb/miniconda3/envs/micc/lib/R/library/BH/include/boost/config/detail/posix_features.hpp:18:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:658:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/gethostuuid.h:39:17: error: unknown type name 'uuid_t'
int gethostuuid(uuid_t, const struct timespec *) __OSX_AVAILABLE_STARTING(__MAC_10_5, __IPHONE_NA);
                ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/dplyr.h:4:
In file included from ../inst/include/dplyr/main.h:6:
In file included from ../inst/include/dplyr/workarounds/static_assert.h:17:
In file included from /Users/jusdeb/miniconda3/envs/micc/lib/R/library/BH/include/boost/config.hpp:57:
In file included from /Users/jusdeb/miniconda3/envs/micc/lib/R/library/BH/include/boost/config/platform/macos.hpp:28:
In file included from /Users/jusdeb/miniconda3/envs/micc/lib/R/library/BH/include/boost/config/detail/posix_features.hpp:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:665:27: error: unknown type name 'uuid_t'; did you mean 'uid_t'?
int      getsgroups_np(int *, uuid_t);
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_uid_t.h:31:31: note: 'uid_t' declared here
typedef __darwin_uid_t        uid_t;
                              ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/dplyr.h:4:
In file included from ../inst/include/dplyr/main.h:6:
In file included from ../inst/include/dplyr/workarounds/static_assert.h:17:
In file included from /Users/jusdeb/miniconda3/envs/micc/lib/R/library/BH/include/boost/config.hpp:57:
In file included from /Users/jusdeb/miniconda3/envs/micc/lib/R/library/BH/include/boost/config/platform/macos.hpp:28:
In file included from /Users/jusdeb/miniconda3/envs/micc/lib/R/library/BH/include/boost/config/detail/posix_features.hpp:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:667:27: error: unknown type name 'uuid_t'; did you mean 'uid_t'?
int      getwgroups_np(int *, uuid_t);
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_uid_t.h:31:31: note: 'uid_t' declared here
typedef __darwin_uid_t        uid_t;
                              ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/dplyr.h:4:
In file included from ../inst/include/dplyr/main.h:6:
In file included from ../inst/include/dplyr/workarounds/static_assert.h:17:
In file included from /Users/jusdeb/miniconda3/envs/micc/lib/R/library/BH/include/boost/config.hpp:57:
In file included from /Users/jusdeb/miniconda3/envs/micc/lib/R/library/BH/include/boost/config/platform/macos.hpp:28:
In file included from /Users/jusdeb/miniconda3/envs/micc/lib/R/library/BH/include/boost/config/detail/posix_features.hpp:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:730:31: error: unknown type name 'uuid_t'; did you mean 'uid_t'?
int      setsgroups_np(int, const uuid_t);
                                  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_uid_t.h:31:31: note: 'uid_t' declared here
typedef __darwin_uid_t        uid_t;
                              ^
In file included from RcppExports.cpp:4:
In file included from ./../inst/include/dplyr.h:4:
In file included from ../inst/include/dplyr/main.h:6:
In file included from ../inst/include/dplyr/workarounds/static_assert.h:17:
In file included from /Users/jusdeb/miniconda3/envs/micc/lib/R/library/BH/include/boost/config.hpp:57:
In file included from /Users/jusdeb/miniconda3/envs/micc/lib/R/library/BH/include/boost/config/platform/macos.hpp:28:
In file included from /Users/jusdeb/miniconda3/envs/micc/lib/R/library/BH/include/boost/config/detail/posix_features.hpp:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:732:31: error: unknown type name 'uuid_t'; did you mean 'uid_t'?
int      setwgroups_np(int, const uuid_t);
                                  ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/_types/_uid_t.h:31:31: note: 'uid_t' declared here
typedef __darwin_uid_t        uid_t;
                              ^
5 errors generated.
make: *** [/Users/jusdeb/miniconda3/envs/micc/lib/R/etc/Makeconf:167: RcppExports.o] Error 1
ERROR: compilation failed for package ‘dplyr’
* removing ‘/Users/jusdeb/miniconda3/envs/micc/lib/R/library/dplyr’
* restoring previous ‘/Users/jusdeb/miniconda3/envs/micc/lib/R/library/dplyr’
Error: Failed to install 'breakaway' from GitHub:
  (converted from warning) installation of package ‘dplyr’ had non-zero exit status
Execution halted
Traceback (most recent call last):
  File "/Users/jusdeb/miniconda3/envs/micc/lib/python3.6/site-packages/q2cli/commands.py", line 328, in __call__
    results = action(**arguments)
  File "</Users/jusdeb/miniconda3/envs/micc/lib/python3.6/site-packages/decorator.py:decorator-gen-477>", line 2, in alpha
  File "/Users/jusdeb/miniconda3/envs/micc/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
    output_types, provenance)
  File "/Users/jusdeb/miniconda3/envs/micc/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/Users/jusdeb/miniconda3/envs/micc/lib/python3.6/site-packages/q2_breakaway/_alphas.py", line 54, in alpha
    run_commands([cmd])
  File "/Users/jusdeb/miniconda3/envs/micc/lib/python3.6/site-packages/q2_breakaway/_alphas.py", line 37, in run_commands
    subprocess.run(cmd, check=True)
  File "/Users/jusdeb/miniconda3/envs/micc/lib/python3.6/subprocess.py", line 418, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_new_richness.R', '/var/folders/bw/q064ds0d2795_6mxnrssf0l1gkw0rj/T/tmp79usq_in/table.tsv', '/var/folders/bw/q064ds0d2795_6mxnrssf0l1gkw0rj/T/q2-AlphaDiversityFormat-ne3fy66f']' returned non-zero exit status 1.

Plugin error from breakaway:

  Command '['run_new_richness.R', '/var/folders/bw/q064ds0d2795_6mxnrssf0l1gkw0rj/T/tmp79usq_in/table.tsv', '/var/folders/bw/q064ds0d2795_6mxnrssf0l1gkw0rj/T/q2-AlphaDiversityFormat-ne3fy66f']' returned non-zero exit status 1.

See above for debug info.
2 Likes

I think the core error is

error: unknown type name 'uuid_t'; did you mean 'uid_t'?

I found this same issue for dplyr: https://community.rstudio.com/t/dplyr-installation-issues/58111/2
And this github comment: https://github.com/r-lib/fs/issues/256#issuecomment-602258833.

Do those help?

Does q2-Breakaway ship in a prebuilt conda package, because this looks like it’s building from source?

Colin

1 Like

Hi @colinbrislawn,

Thanks! This is really helpful.

I’ve tried installing dyplr previously in a similar environment, and ran into a similar issue. It didnt work with the conda build or with the R build, for some reason. Ive been getting a lot of weird complier issues recently. :confused: So, Im not sure if a conda installation will work, but I’ll try it and report back!

Best,
Justine

1 Like

I gave up on cran and checkpoint()/mran about 6 months ago.

conda config --add channels conda-forge
conda config --add channels defaults
conda config --add channels r
conda config --add channels bioconda
conda install rstudio
conda install r-tidyverse

It’s changed my life!

But when build issues do crop up, I’m not much of an expert :crying_cat_face:

2 Likes