Comments (8)
RogerGinBer
commented on June 19, 2024
Hi Emily,
I've compiled the vignette again but I haven't been able to replicate the error. Looking at the error message, I suspect it has to do with XCMS versioning, could you please run sessionInfo() and paste the result?
from rhermes.
Emilyzwu
commented on June 19, 2024
Hi Roger,
Thanks for you reply! It seems that I have lots of packages not attached or updated properly lol - I did notice that whilst I was installing RHermes last week and some packages/dependencies kept failing to be updated so I was wondering if that is something to do with the R ver. that I'm using (3.5.3). BTW, I wasn't able to install keras and tensorflow neither (the miniconda works tho) and thus can't launch RHermesGUI(); is it also to do with my R version?
sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RHermes_0.99.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 compiler_3.5.3 pillar_1.6.4 XVector_0.22.0
[5] keras_2.7.0 base64enc_0.1-3 tools_3.5.3 zlibbioc_1.28.0
[9] zeallot_0.1.0 digest_0.6.29 lattice_0.20-38 viridisLite_0.4.0
[13] jsonlite_1.6.1 lifecycle_1.0.1 tibble_3.0.1 gtable_0.3.0
[17] pkgconfig_2.0.3 png_0.1-7 rlang_0.4.12 Matrix_1.2-15
[21] igraph_1.2.5 parallel_3.5.3 fastmap_1.1.0 httr_1.4.2
[25] dplyr_0.8.5 generics_0.1.1 Biostrings_2.50.2 S4Vectors_0.20.1
[29] vctrs_0.3.8 htmlwidgets_1.5.4 IRanges_2.16.0 stats4_3.5.3
[33] grid_3.5.3 tidyselect_1.0.0 reticulate_1.15 glue_1.6.0
[37] data.table_1.12.8 R6_2.5.1 plotly_4.10.0 philentropy_0.4.0
[41] fansi_0.4.0 BiocParallel_1.16.6 whisker_0.4 tidyr_1.0.2
[45] ggplot2_3.2.0 purrr_0.3.4 magrittr_1.5 tfruns_1.5.0
[49] htmltools_0.5.2 scales_1.1.1 ellipsis_0.3.2 networkD3_0.4
[53] BiocGenerics_0.28.0 KEGGREST_1.22.0 assertthat_0.2.1 colorspace_1.4-1
[57] tensorflow_2.7.0 utf8_1.1.4 visNetwork_2.1.0 lazyeval_0.2.2
[61] munsell_0.5.0 crayon_1.4.2
from rhermes.
RogerGinBer
commented on June 19, 2024
Hi Emily,
It seems that the R version you're using might be the cause of the errors you've been experiencing. Recent dependencies releases require R >= 4.0.0, so that's the reason you can't update them anymore. I'd strongly suggest you update your R version and reinstall the packages.
The original error you got stems from xcms function PeaksWithCentwave, which we use to split long SOIs into smaller peaks whenever possible. If your installation is correct, the following code should return an empty matrix and raise a warning saying no peaks were found (but not an error):
xcms::peaksWithCentWave(int = 1:10, rt = 1:10)
Regarding the GUI not launching, I think it's also a problem with the dependencies/R version, but it's a bit strange since the sessionInfo() shows keras and tensorflow as loaded (and thus, installed). Could you share the error message you're getting when running RHermesGUI()? I'll be glad to help 👍
from rhermes.
Emilyzwu
commented on June 19, 2024
Hi Roger,
Thank you so much!
Yes it seems to be the R version issue. I downloaded the R 4.1.2 and re-install RHermes, problem solved! And GUI works as well.
However, I still can't get the keras and tensorflow work:
keras::install_keras()
Collecting package metadata (current_repodata.json): ...working... failed
>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\exceptions.py", line 1079, in __call__
return func(*args, **kwargs)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\cli\main.py", line 84, in _main
exit_code = do_call(args, p)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\cli\conda_argparse.py", line 83, in do_call
return getattr(module, func_name)(args, parser)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\cli\main_create.py", line 41, in execute
install(args, parser, 'create')
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\cli\install.py", line 261, in install
unlink_link_transaction = solver.solve_for_transaction(
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\solve.py", line 114, in solve_for_transaction
unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\solve.py", line 157, in solve_for_diff
final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\solve.py", line 262, in solve_final_state
ssc = self._collect_all_metadata(ssc)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\common\io.py", line 88, in decorated
return f(*args, **kwds)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\solve.py", line 425, in _collect_all_metadata
index, r = self._prepare(prepared_specs)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\solve.py", line 1020, in _prepare
reduced_index = get_reduced_index(self.prefix, self.channels,
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\index.py", line 288, in get_reduced_index
new_records = SubdirData.query_all(spec, channels=channels, subdirs=subdirs,
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\subdir_data.py", line 140, in query_all
result = tuple(concat(executor.map(subdir_query, channel_urls)))
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\concurrent\futures\_base.py", line 608, in result_iterator
yield fs.pop().result()
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\concurrent\futures\_base.py", line 445, in result
return self.__get_result()
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\concurrent\futures\_base.py", line 390, in __get_result
raise self._exception
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\concurrent\futures\thread.py", line 52, in run
result = self.fn(*self.args, **self.kwargs)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\subdir_data.py", line 132, in <lambda>
subdir_query = lambda url: tuple(SubdirData(Channel(url), repodata_fn=repodata_fn).query(
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\subdir_data.py", line 145, in query
self.load()
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\subdir_data.py", line 210, in load
_internal_state = self._load()
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\subdir_data.py", line 375, in _load
raw_repodata_str = fetch_repodata_remote_request(
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\subdir_data.py", line 701, in fetch_repodata_remote_request
resp = session.get(join_url(url, filename), headers=headers, proxies=session.proxies,
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\requests\sessions.py", line 555, in get
return self.request('GET', url, **kwargs)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\requests\sessions.py", line 542, in request
resp = self.send(prep, **send_kwargs)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\requests\sessions.py", line 655, in send
r = adapter.send(request, **kwargs)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\requests\adapters.py", line 439, in send
resp = conn.urlopen(
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\urllib3\connectionpool.py", line 696, in urlopen
self._prepare_proxy(conn)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\urllib3\connectionpool.py", line 964, in _prepare_proxy
conn.connect()
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\urllib3\connection.py", line 359, in connect
conn = self._connect_tls_proxy(hostname, conn)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\urllib3\connection.py", line 500, in _connect_tls_proxy
return ssl_wrap_socket(
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\urllib3\util\ssl_.py", line 453, in ssl_wrap_socket
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\urllib3\util\ssl_.py", line 495, in _ssl_wrap_socket_impl
return ssl_context.wrap_socket(sock)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\ssl.py", line 500, in wrap_socket
return self.sslsocket_class._create(
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\ssl.py", line 997, in _create
raise ValueError("check_hostname requires server_hostname")
ValueError: check_hostname requires server_hostname
$ C:\Users\Emily\AppData\Local\R-MINI~1\Scripts\conda-script.py create --yes --prefix C:/Users/Emily/AppData/Local/r-miniconda/envs/r-reticulate python=3.6 numpy -c conda-forge
environment variables:
CIO_TEST=
CONDA_EXE=C:\Users\Emily\AppData\Local\R-MINI1\condabin..\Scripts\conda.exe1\condabin..\Scripts\conda.exe"
CONDA_EXES="C:\Users\Emily\AppData\Local\R-MINI
CONDA_ROOT=C:\Users\Emily\AppData\Local\R-MINI11;C:\Users\Emily\AppData\Local\R-M
CURL_CA_BUNDLE=
HOMEPATH=\Users\Emily
PATH=C:\Users\Emily\AppData\Local\R-MINI
INI1\Library\mingw-w64\bin;C:\Users\Emily\AppData\Local\R-MINI1\Libr
ary\usr\bin;C:\Users\Emily\AppData\Local\R-MINI1\Library\bin;C:\Users1\Scripts;C:\Users\Emily\AppData\Local\R-M
\Emily\AppData\Local\R-MINI
INI~1\bin;C:\Program Files\R\R-4.1.2\bin\x64;C:\Program Files
(x86)\Common Files\Oracle\Java\javapath;C:\Windows\system32;C:\Windows
;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0;
C:\Program Files (x86)\Common Files\lenovo\easyplussdk\bin;C:\Program
Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program
Files\Intel\WiFi\bin;C:\Program Files\Common Files\Intel\WirelessComm
on;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS
\System32\WindowsPowerShell\v1.0;C:\WINDOWS\System32\OpenSSH;C:\User
s\Emily\AppData\Local\Microsoft\WindowsApps;
PSMODULEPATH=C:\Program Files\WindowsPowerShell\Modules;C:\WINDOWS\system32\Windows
PowerShell\v1.0\Modules
REQUESTS_CA_BUNDLE=
RMARKDOWN_MATHJAX_PATH=C:/Program Files/RStudio/resources/mathjax-26
RS_RPOSTBACK_PATH=C:/Program Files/RStudio/bin/rpostback
SSL_CERT_FILE=
active environment : None
user config file : C:\Users\Emily\.condarc
populated config files :
conda version : 4.10.3
conda-build version : not installed
python version : 3.9.5.final.0
virtual packages : __cuda=8.0=0
__win=0=0
__archspec=1=x86_64
base environment : C:\Users\Emily\AppData\Local\R-MINI1 (writable)1\etc\conda
conda av data dir : C:\Users\Emily\AppData\Local\R-MINI
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/win-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/win-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/win-64
https://repo.anaconda.com/pkgs/r/noarch
https://repo.anaconda.com/pkgs/msys2/win-64
https://repo.anaconda.com/pkgs/msys2/noarch
package cache : C:\Users\Emily\AppData\Local\R-MINI1\pkgs1\envs
C:\Users\Emily.conda\pkgs
C:\Users\Emily\AppData\Local\conda\conda\pkgs
envs directories : C:\Users\Emily\AppData\Local\R-MINI
C:\Users\Emily.conda\envs
C:\Users\Emily\AppData\Local\conda\conda\envs
platform : win-64
user-agent : conda/4.10.3 requests/2.25.1 CPython/3.9.5 Windows/10 Windows/10.0.19042
administrator : False
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
Upload did not complete.
Error: Error 1 occurred creating conda environment C:/Users/Emily/AppData/Local/r-miniconda/envs/r-reticulate
tensorflow::install_tensorflow()
Collecting package metadata (current_repodata.json): ...working... failed
>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\exceptions.py", line 1079, in __call__
return func(*args, **kwargs)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\cli\main.py", line 84, in _main
exit_code = do_call(args, p)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\cli\conda_argparse.py", line 83, in do_call
return getattr(module, func_name)(args, parser)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\cli\main_create.py", line 41, in execute
install(args, parser, 'create')
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\cli\install.py", line 261, in install
unlink_link_transaction = solver.solve_for_transaction(
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\solve.py", line 114, in solve_for_transaction
unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\solve.py", line 157, in solve_for_diff
final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\solve.py", line 262, in solve_final_state
ssc = self._collect_all_metadata(ssc)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\common\io.py", line 88, in decorated
return f(*args, **kwds)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\solve.py", line 425, in _collect_all_metadata
index, r = self._prepare(prepared_specs)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\solve.py", line 1020, in _prepare
reduced_index = get_reduced_index(self.prefix, self.channels,
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\index.py", line 288, in get_reduced_index
new_records = SubdirData.query_all(spec, channels=channels, subdirs=subdirs,
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\subdir_data.py", line 140, in query_all
result = tuple(concat(executor.map(subdir_query, channel_urls)))
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\concurrent\futures\_base.py", line 608, in result_iterator
yield fs.pop().result()
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\concurrent\futures\_base.py", line 445, in result
return self.__get_result()
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\concurrent\futures\_base.py", line 390, in __get_result
raise self._exception
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\concurrent\futures\thread.py", line 52, in run
result = self.fn(*self.args, **self.kwargs)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\subdir_data.py", line 132, in <lambda>
subdir_query = lambda url: tuple(SubdirData(Channel(url), repodata_fn=repodata_fn).query(
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\subdir_data.py", line 145, in query
self.load()
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\subdir_data.py", line 210, in load
_internal_state = self._load()
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\subdir_data.py", line 375, in _load
raw_repodata_str = fetch_repodata_remote_request(
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\conda\core\subdir_data.py", line 701, in fetch_repodata_remote_request
resp = session.get(join_url(url, filename), headers=headers, proxies=session.proxies,
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\requests\sessions.py", line 555, in get
return self.request('GET', url, **kwargs)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\requests\sessions.py", line 542, in request
resp = self.send(prep, **send_kwargs)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\requests\sessions.py", line 655, in send
r = adapter.send(request, **kwargs)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\requests\adapters.py", line 439, in send
resp = conn.urlopen(
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\urllib3\connectionpool.py", line 696, in urlopen
self._prepare_proxy(conn)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\urllib3\connectionpool.py", line 964, in _prepare_proxy
conn.connect()
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\urllib3\connection.py", line 359, in connect
conn = self._connect_tls_proxy(hostname, conn)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\urllib3\connection.py", line 500, in _connect_tls_proxy
return ssl_wrap_socket(
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\urllib3\util\ssl_.py", line 453, in ssl_wrap_socket
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\site-packages\urllib3\util\ssl_.py", line 495, in _ssl_wrap_socket_impl
return ssl_context.wrap_socket(sock)
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\ssl.py", line 500, in wrap_socket
return self.sslsocket_class._create(
File "C:\Users\Emily\AppData\Local\R-MINI~1\lib\ssl.py", line 997, in _create
raise ValueError("check_hostname requires server_hostname")
ValueError: check_hostname requires server_hostname
$ C:\Users\Emily\AppData\Local\R-MINI~1\Scripts\conda-script.py create --yes --prefix C:/Users/Emily/AppData/Local/r-miniconda/envs/r-reticulate python=3.6 numpy -c conda-forge
environment variables:
CIO_TEST=
CONDA_EXE=C:\Users\Emily\AppData\Local\R-MINI1\condabin..\Scripts\conda.exe1\condabin..\Scripts\conda.exe"
CONDA_EXES="C:\Users\Emily\AppData\Local\R-MINI
CONDA_ROOT=C:\Users\Emily\AppData\Local\R-MINI11;C:\Users\Emily\AppData\Local\R-M
CURL_CA_BUNDLE=
HOMEPATH=\Users\Emily
PATH=C:\Users\Emily\AppData\Local\R-MINI
INI1\Library\mingw-w64\bin;C:\Users\Emily\AppData\Local\R-MINI1\Libr
ary\usr\bin;C:\Users\Emily\AppData\Local\R-MINI1\Library\bin;C:\Users1\Scripts;C:\Users\Emily\AppData\Local\R-M
\Emily\AppData\Local\R-MINI
INI~1\bin;C:\Program Files\R\R-4.1.2\bin\x64;C:\Program Files
(x86)\Common Files\Oracle\Java\javapath;C:\Windows\system32;C:\Windows
;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0;
C:\Program Files (x86)\Common Files\lenovo\easyplussdk\bin;C:\Program
Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program
Files\Intel\WiFi\bin;C:\Program Files\Common Files\Intel\WirelessComm
on;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS
\System32\WindowsPowerShell\v1.0;C:\WINDOWS\System32\OpenSSH;C:\User
s\Emily\AppData\Local\Microsoft\WindowsApps;
PSMODULEPATH=C:\Program Files\WindowsPowerShell\Modules;C:\WINDOWS\system32\Windows
PowerShell\v1.0\Modules
REQUESTS_CA_BUNDLE=
RMARKDOWN_MATHJAX_PATH=C:/Program Files/RStudio/resources/mathjax-26
RS_RPOSTBACK_PATH=C:/Program Files/RStudio/bin/rpostback
SSL_CERT_FILE=
active environment : None
user config file : C:\Users\Emily\.condarc
populated config files :
conda version : 4.10.3
conda-build version : not installed
python version : 3.9.5.final.0
virtual packages : __cuda=8.0=0
__win=0=0
__archspec=1=x86_64
base environment : C:\Users\Emily\AppData\Local\R-MINI1 (writable)1\etc\conda
conda av data dir : C:\Users\Emily\AppData\Local\R-MINI
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/win-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/win-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/win-64
https://repo.anaconda.com/pkgs/r/noarch
https://repo.anaconda.com/pkgs/msys2/win-64
https://repo.anaconda.com/pkgs/msys2/noarch
package cache : C:\Users\Emily\AppData\Local\R-MINI1\pkgs1\envs
C:\Users\Emily.conda\pkgs
C:\Users\Emily\AppData\Local\conda\conda\pkgs
envs directories : C:\Users\Emily\AppData\Local\R-MINI
C:\Users\Emily.conda\envs
C:\Users\Emily\AppData\Local\conda\conda\envs
platform : win-64
user-agent : conda/4.10.3 requests/2.25.1 CPython/3.9.5 Windows/10 Windows/10.0.19042
administrator : False
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
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Error: Error 1 occurred creating conda environment C:/Users/Emily/AppData/Local/r-miniconda/envs/r-reticulate
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Emilyzwu
commented on June 19, 2024
And weirdly, I did find both the keras and tensorflow folder in my R library.
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RogerGinBer
commented on June 19, 2024
Hi Emily,
The R packages keras and tensorflow serve just as interfaces to work with the Python installation, which is the one giving you the errors above. Luckily, a working Python installation is no longer required to run RHermes, as we have implemented a simpler blank subtraction method based on cosine elution similarity for when the user doesn't have Python configured. I'll merge the devel branch later today, where I have fixed small bugs regarding that blank subtraction method, so I advise you update.
In case you still want to configure keras and tensorflow, I've found this issue that may be useful (same error code): conda/conda#10590. If you haven't, you could alse give the alternative installation method a try (see README.md), where you open a miniconda terminal (from the Start Menu, it's called Anaconda Prompt) and run:
conda create -n newenv python=3.6 tensorflow keras
When finished, from R you run:
reticulate::use_condaenv("newenv", required = TRUE)
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Emilyzwu
commented on June 19, 2024
Brilliant! Guess I'll just wait for the update :)
I've tried manual installation already and it gave me the similar error msg as shown in R...so I'll just leave it and update the RHermes later.
Wish you a Happy New Year :)
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RogerGinBer
commented on June 19, 2024
Happy New Year!
If there are no further problems, I'll go ahead and close the issue 👍
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