Hello! I am trying to install some packages as below:

BiocManager::install(c('CATALYST'))

but I keep encountering the errors below ("Use secure download method for HTTP" is unchecked and see Renvrion file in etc folder, but not Rprofile, Renviron.site, and Rprofile.site files - found Rprofile file in another folder, but moving it to the etc folder did not work and could not find Renviron.site and Rprofile.site files anywhere):

> BiocManager::install(c('CATALYST'))
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: http://cran.rstudio.com/
Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
Installing package(s) 'CATALYST'
also installing the dependencies 'densvis', 'scater'

Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-x86_64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-x86_64/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-x86_64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-x86_64/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/books/bin/macosx/big-sur-x86_64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/books/bin/macosx/big-sur-x86_64/contrib/4.3/PACKAGES'
Package which is only available in source form, and may need
  compilation of C/C++/Fortran: 'densvis'
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source packages 'densvis', 'scater', 'CATALYST'

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/densvis_1.10.1.tar.gz'
Content type 'application/x-gzip' length 1720069 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/scater_1.28.0.tar.gz'
Content type 'application/x-gzip' length 4089325 bytes (3.9 MB)
==================================================
downloaded 3.9 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/CATALYST_1.24.0.tar.gz'
Content type 'application/x-gzip' length 10825510 bytes (10.3 MB)
==================================================
downloaded 10.3 MB

* installing *source* package 'densvis' ...
** using non-staged installation via StagedInstall field
** libs
using C++ compiler: 'Apple clang version 12.0.5 (clang-1205.0.22.9)'
using C++14
using SDK: 'MacOSX11.3.sdk'
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c densne.cpp -o densne.o
densne.cpp:181:24: warning: variable 'row_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:201:33: note: uninitialized use occurs here
    computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
                                ^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:154:35: note: initialize the variable 'row_P' to silence this warning
    double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
                                  ^
                                   = nullptr
densne.cpp:181:24: warning: variable 'col_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:201:40: note: uninitialized use occurs here
    computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
                                       ^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:154:56: note: initialize the variable 'col_P' to silence this warning
    double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
                                                       ^
                                                        = nullptr
densne.cpp:181:24: warning: variable 'val_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:201:47: note: uninitialized use occurs here
    computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
                                              ^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:154:71: note: initialize the variable 'val_P' to silence this warning
    double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
                                                                      ^
                                                                       = nullptr
densne.cpp:181:24: warning: variable 'val_D' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:201:54: note: uninitialized use occurs here
    computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
                                                     ^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:154:86: note: initialize the variable 'val_D' to silence this warning
    double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
                                                                                     ^
                                                                                      = nullptr

4 warnings generated.
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c densvis.cpp -o densvis.o
clang++ -arch x86_64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sptree.cpp -o sptree.o
clang++ -arch x86_64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o densvis.so RcppExports.o densne.o densvis.o sptree.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation

ld: warning: directory not found for option '-L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0'
ld: warning: directory not found for option '-L/opt/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [densvis.so] Error 1

ERROR: compilation failed for package 'densvis'
* removing '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/densvis'
ERROR: dependency 'densvis' is not available for package 'scater'
* removing '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/scater'
ERROR: dependency 'scater' is not available for package 'CATALYST'
* removing '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/CATALYST'

The downloaded source packages are in
    'private/var/folders/75/1q40jjvs3pjd22q4630w41dwwm6wh2/T/RtmpmYxF0i/downloaded_packages'
Old packages: 'Matrix'
Update all/some/none? [a/s/n]: a

Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-x86_64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/data/experiment/bin/macosx/big-sur-x86_64/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-x86_64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/workflows/bin/macosx/big-sur-x86_64/contrib/4.3/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/books/bin/macosx/big-sur-x86_64/contrib/4.3:
  cannot open URL 'https://bioconductor.org/packages/3.17/books/bin/macosx/big-sur-x86_64/contrib/4.3/PACKAGES'
trying URL 'http://cran.rstudio.com/bin/macosx/big-sur-x86_64/contrib/4.3/Matrix_1.5-4.tgz'
Content type 'application/x-gzip' length 5886784 bytes (5.6 MB)
==================================================
downloaded 5.6 MB


The downloaded binary packages are in
    /var/folders/75/1q40jjvs3pjd22q4630w41dwwm6wh2/T//RtmpmYxF0i/downloaded_packages
Warning messages:
1: In install.packages(...) :
  installation of package 'densvis' had non-zero exit status
2: In install.packages(...) :
  installation of package 'scater' had non-zero exit status
3: In install.packages(...) :
  installation of package 'CATALYST' had non-zero exit status

> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocManager_1.30.20

loaded via a namespace (and not attached):
[1] compiler_4.3.0 tools_4.3.0

The error isn't finding the repo but finding your fortran headers. I don't use MacOS, so cannot say for sure, but this appears to be something you could try.

I found that using Google, BTW, which is a good skill to cultivate.

Should be fixed now. Can you try again?

Note that these warnings are benign and did not affect BiocManager::install()'s ability to find packages.

Best,

H.