shared object ‘fastbaps.dylib’ not found

[gtonkinhill]

shared object ‘fastbaps.dylib’ not found

[gtonkinhill]

Hi, apologies for the slow response. It might be worth trying to reinstall Rcpp using install.packages('Rcpp') before installing fastbaps. This issue can sometimes also be fixed by restarting R.

[jhawkey]

Hi, I am also having this issue with the conda install (Mac OS 10.15.4). I have tried to reinstall Rcpp as suggested, but got the following error:

ld: unknown option: -platform_version
clang-10: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [/Users/jane/miniconda3/envs/fastbaps/lib/R/share/make/shlib.mk:6: Rcpp.dylib] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/Users/jane/miniconda3/envs/fastbaps/lib/R/library/Rcpp’
* restoring previous ‘/Users/jane/miniconda3/envs/fastbaps/lib/R/library/Rcpp’

I also tried restarting R but haven't had any luck unfortunately.

I get the same error when attempting to use the run_fastbaps command line tool.

Any help would be greatly appreciated!

[gtonkinhill]

Thanks for flagging this. It looks like something strange is going on with the way conda is handling the c++ dependencies. I will try and take a look in the next day or so. The run_fastbaps command relies on the main library being installed so wont work if that has failed.

Conda and R are often a bit tricky as sometimes local R versions can interfere. Are you able to install the program without conda using devtools::install_github("gtonkinhill/fastbaps") ?

[jhawkey]

Unfortunately I wasn't able to install in R either. I tried the install in a new packrat project to ensure I wasn't getting conflicts with other R packages that I have installed. I also had a look at the other issues raised with installs in R, and attempted to fix it by running

install.packages("Rcpp")
install.packages("RcppArmadillo")

as mentioned in #9, but that didn't help either unfortunately. I also tried the xcode command listed at the bottom of that issue, but my xcode is up to date (according to xcode).

The errors I was getting were different to those in #9, I have reproduced the compilation output in full below.

> devtools::install_github("gtonkinhill/fastbaps")
Downloading GitHub repo gtonkinhill/fastbaps@master
✓  checking for file ‘/private/var/folders/_w/q60cr5_n3ts6561n1dpl_pvw0000gn/T/RtmpNCSCk9/remotes753c509a0346/gtonkinhill-fastbaps-4b70f3f/DESCRIPTION’ ...
─  preparing ‘fastbaps’:
✓  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 ‘fastbaps_1.0.0.tar.gz’
   
Installing package into ‘/Users/jane/Dropbox/ShigellaSonneiGenotyping/paper/fastbaps_analysis/packrat/lib/x86_64-apple-darwin15.6.0/3.5.3’
(as ‘lib’ is unspecified)
* installing *source* package ‘fastbaps’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Users/jane/Dropbox/ShigellaSonneiGenotyping/paper/fastbaps_analysis/packrat/lib/x86_64-apple-darwin15.6.0/3.5.3/Rcpp/include" -I"/Users/jane/Dropbox/ShigellaSonneiGenotyping/paper/fastbaps_analysis/packrat/lib/x86_64-apple-darwin15.6.0/3.5.3/RcppArmadillo/include" -I/usr/local/include  -DARMA_64BIT_WORD -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Users/jane/Dropbox/ShigellaSonneiGenotyping/paper/fastbaps_analysis/packrat/lib/x86_64-apple-darwin15.6.0/3.5.3/Rcpp/include" -I"/Users/jane/Dropbox/ShigellaSonneiGenotyping/paper/fastbaps_analysis/packrat/lib/x86_64-apple-darwin15.6.0/3.5.3/RcppArmadillo/include" -I/usr/local/include  -DARMA_64BIT_WORD -fPIC  -Wall -g -O2 -c bhier.cpp -o bhier.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Users/jane/Dropbox/ShigellaSonneiGenotyping/paper/fastbaps_analysis/packrat/lib/x86_64-apple-darwin15.6.0/3.5.3/Rcpp/include" -I"/Users/jane/Dropbox/ShigellaSonneiGenotyping/paper/fastbaps_analysis/packrat/lib/x86_64-apple-darwin15.6.0/3.5.3/RcppArmadillo/include" -I/usr/local/include  -DARMA_64BIT_WORD -fPIC  -Wall -g -O2 -c bhier_parallel.cpp -o bhier_parallel.o
bhier_parallel.cpp:35:22: warning: unused variable 'p1' [-Wunused-variable]
  unsigned int i,j,p,p1,p2;
                     ^
bhier_parallel.cpp:35:25: warning: unused variable 'p2' [-Wunused-variable]
  unsigned int i,j,p,p1,p2;
                        ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Users/jane/Dropbox/ShigellaSonneiGenotyping/paper/fastbaps_analysis/packrat/lib/x86_64-apple-darwin15.6.0/3.5.3/Rcpp/include" -I"/Users/jane/Dropbox/ShigellaSonneiGenotyping/paper/fastbaps_analysis/packrat/lib/x86_64-apple-darwin15.6.0/3.5.3/RcppArmadillo/include" -I/usr/local/include  -DARMA_64BIT_WORD -fPIC  -Wall -g -O2 -c calc_ddk.cpp -o calc_ddk.o
calc_ddk.cpp:19:7: warning: unused variable 'n_snps' [-Wunused-variable]
  int n_snps = snp_matrix.n_rows;
      ^
calc_ddk.cpp:22:18: warning: unused variable 'j' [-Wunused-variable]
  unsigned int i,j,m,partition_length,left,right;
                 ^
calc_ddk.cpp:22:22: warning: unused variable 'partition_length' [-Wunused-variable]
  unsigned int i,j,m,partition_length,left,right;
                     ^
calc_ddk.cpp:23:7: warning: unused variable 'count' [-Wunused-variable]
  int count = 0;
      ^
4 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Users/jane/Dropbox/ShigellaSonneiGenotyping/paper/fastbaps_analysis/packrat/lib/x86_64-apple-darwin15.6.0/3.5.3/Rcpp/include" -I"/Users/jane/Dropbox/ShigellaSonneiGenotyping/paper/fastbaps_analysis/packrat/lib/x86_64-apple-darwin15.6.0/3.5.3/RcppArmadillo/include" -I/usr/local/include  -DARMA_64BIT_WORD -fPIC  -Wall -g -O2 -c import_fasta_to_vector_each_nt.cpp -o import_fasta_to_vector_each_nt.o
In file included from import_fasta_to_vector_each_nt.cpp:6:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zlib.h:34:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zconf.h:462:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:655:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/gethostuuid.h:39:17: error: C++ requires a type specifier for all declarations
int gethostuuid(uuid_t, const struct timespec *) __OSX_AVAILABLE_STARTING(__MAC_10_5, __IPHONE_NA);
                ^
In file included from import_fasta_to_vector_each_nt.cpp:6:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zlib.h:34:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zconf.h:462:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:662:27: 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 import_fasta_to_vector_each_nt.cpp:6:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zlib.h:34:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zconf.h:462:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:664:27: 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 import_fasta_to_vector_each_nt.cpp:6:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zlib.h:34:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zconf.h:462:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:727:31: 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 import_fasta_to_vector_each_nt.cpp:6:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zlib.h:34:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/zconf.h:462:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/unistd.h:729:31: 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: *** [import_fasta_to_vector_each_nt.o] Error 1
ERROR: compilation failed for package ‘fastbaps’
* removing ‘/Users/jane/Dropbox/ShigellaSonneiGenotyping/paper/fastbaps_analysis/packrat/lib/x86_64-apple-darwin15.6.0/3.5.3/fastbaps’
Error: Failed to install 'fastbaps' from GitHub:
  (converted from warning) installation of package ‘/var/folders/_w/q60cr5_n3ts6561n1dpl_pvw0000gn/T//RtmpNCSCk9/file753c69e3d3cc/fastbaps_1.0.0.tar.gz’ had non-zero exit status

[gtonkinhill]

Ah I think I may have run into this previously. It was a mac specific issue with Rcpp and was possible to fix by installing the dev version of Rcpp as suggested here. However, I think a new release of Rcpp was created 2 days ago which may include the fix. Are you able to try updating Rcpp using devtools::install_github("RcppCore/Rcpp")

I am still looking into what might be going on with the conda version.

[jhawkey]

Ah excellent! That appears to have solved my problem. Thank you!