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Sage-Bionetworks / synapser

An R package providing programmatic access to Synapse
Apache License 2.0
32 stars 21 forks source link

Unable to Install Synapser #321

Closed JManickam13 closed 10 months ago

JManickam13 commented 1 year ago

Operating system

I am working on a Mac OSX operating on an M1 chip.

Description of the problem

I am trying to install synapser into R Studio using the install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org")) command and I end up having a large error message detailing dependency conflicts that I am unsure of how to resolve

Expected behavior

I am not sure exactly how it should look but I do know it is supposed to download correctly.

Actual behavior

`UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

Your python: python=3.11

If python is on the left-most side of the chain, that's the version you've asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that.

The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package cryptography conflicts for: requests[version='<3'] -> urllib3[version='>=1.21.1,<1.26,!=1.25.0,!=1.25.1'] -> cryptography[version='>=1.3.4'] pysftp -> paramiko[version='>=1.17.0'] -> cryptography[version='>=1.1|>=1.5|>=2.5']

Package tzdata conflicts for: requests[version='<3'] -> python[version='>=3.10,<3.11.0a0'] -> tzdata jinja2 -> python[version='>=3.11,<3.12.0a0'] -> tzdata pandas[version='<1.5'] -> pypy3.9[version='>=7.3.9'] -> tzdata markupsafe -> python[version='>=3.11,<3.12.0a0'] -> tzdata python=3.11 -> tzdata

Package libsqlite conflicts for: python=3.11 -> libsqlite[version='>=3.39.4,<4.0a0|>=3.40.0,<4.0a0|>=3.42.0,<4.0a0'] python=3.11 -> sqlite[version='>=3.41.2,<4.0a0'] -> libsqlite[version='3.41.2|3.42.0',build='h58db7d2_1|h58db7d2_0']

Package setuptools conflicts for: pandas[version='<1.5'] -> numexpr[version='>=2.7.1'] -> setuptools python=3.11 -> pip -> setuptools jinja2 -> setuptools pandas[version='<1.5'] -> setuptools[version='<60.0.0']

Package python_abi conflicts for: requests[version='<3'] -> python_abi[version='2.7.|3.6.|3.6|3.8.|3.7.',build='_cp27m|_cp37m|_pypy36_pp73|_cp38|_cp36m'] requests[version='<3'] -> certifi[version='>=2017.4.17'] -> python_abi[version='3.10.|3.9|3.8|3.9.|3.7',build='_pypy37_pp73|_cp39|_pypy39_pp73|_cp310|_pypy38_pp73'] pandas[version='<1.5'] -> numpy[version='>=1.19.5,<2.0a0'] -> python_abi=3.11[build=_cp311] markupsafe -> python_abi[version='2.7.|3.10.|3.11.|3.8|3.9.|3.9|3.8.|3.7.|3.7|3.6|3.6.',build='_cp27m|_pypy37_pp73|_cp310|_pypy39_pp73|_cp311|_pypy38_pp73|_cp39|_cp38|_cp37m|_pypy36_pp73|_cp36m'] pysftp -> python=3.6 -> python_abi==3.6[build=_pypy36_pp73] pandas[version='<1.5'] -> python_abi[version='3.10.|3.8.|3.8|3.9|3.9.|3.7|3.7.|3.6|3.6.',build='_pypy37_pp73|_cp310|_pypy39_pp73|_pypy38_pp73|_cp39|_cp38|_cp37m|_pypy36_pp73|_cp36m'] jinja2 -> markupsafe[version='>=0.23,<2'] -> python_abi[version='2.7.|3.10.|3.7.|3.7|3.9.|3.8.|3.6|3.6.|3.8|3.9|3.11.',build='_cp311|_pypy39_pp73|_cp27m|_pypy37_pp73|_cp310|_cp37m|_cp39|_cp38|_pypy36_pp73|_cp36m|_pypy38_pp73']

Package expat conflicts for: markupsafe -> pypy3.8[version='>=7.3.11'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.4.1,<3.0a0|>=2.4.7,<3.0a0|>=2.4.8,<3.0a0|>=2.4.9,<3.0a0|>=2.5.0,<3.0a0|>=2.2.9,<3.0.0a0|>=2.3.0,<3.0a0'] pandas[version='<1.5'] -> pypy3.9[version='>=7.3.9'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.4.8,<3.0a0|>=2.4.9,<3.0a0|>=2.5.0,<3.0a0|>=2.2.9,<3.0.0a0']

Package pypy3.9 conflicts for: markupsafe -> pypy3.9[version='>=7.3.11|>=7.3.9|>=7.3.8'] markupsafe -> python[version='>=3.9,<3.10.0a0'] -> pypy3.9[version='7.3.|7.3.11.|7.3.9.|7.3.8.']

Package pypy3.7 conflicts for: markupsafe -> pypy3.7[version='>=7.3.3|>=7.3.4|>=7.3.7'] markupsafe -> python[version='>=3.7,<3.8.0a0'] -> pypy3.7[version='7.3.|7.3.3.|7.3.4.|7.3.5.|7.3.7.*']

Package pypy3.8 conflicts for: markupsafe -> python[version='>=3.8,<3.9.0a0'] -> pypy3.8[version='7.3.|7.3.11.|7.3.9.|7.3.8.'] markupsafe -> pypy3.8[version='>=7.3.11|>=7.3.9|>=7.3.8'] pandas[version='<1.5'] -> pypy3.8[version='>=7.3.9'] pandas[version='<1.5'] -> numpy[version='>=1.19.5,<2.0a0'] -> pypy3.8[version='7.3.|7.3.11.|>=7.3.11|>=7.3.8|7.3.9.|7.3.8.'] requests[version='<3'] -> certifi[version='>=2017.4.17'] -> pypy3.8[version='7.3.11.|>=7.3.8|>=7.3.9|7.3.9.|7.3.8.'] jinja2 -> setuptools -> pypy3.8[version='7.3.11.|>=7.3.11|>=7.3.8|>=7.3.9|7.3.9.|7.3.8.']

Package certifi conflicts for: requests[version='<3'] -> certifi[version='>=2017.4.17'] pandas[version='<1.5'] -> setuptools[version='<60.0.0'] -> certifi[version='>=2016.09|>=2016.9.26'] jinja2 -> setuptools -> certifi[version='>=2016.09|>=2016.9.26'] requests[version='<3'] -> urllib3[version='>=1.21.1,<1.26,!=1.25.0,!=1.25.1'] -> certifi

Error: one or more Python packages failed to install [error code 1] Execution halted ERROR: configuration failed for package ‘synapser’

The downloaded source packages are in ‘/private/var/folders/6/0r963bdd7r76s46qwrn44hc4s8314r/T/RtmpdvXKJU/downloaded`

Output of sessionInfo()

R version 4.2.2 (2022-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.4.1

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/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] cmapR_1.10.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.11 compiler_4.2.2 pillar_1.9.0
[4] cytolib_2.10.1 GenomeInfoDb_1.34.9 XVector_0.38.0
[7] MatrixGenerics_1.10.0 bitops_1.0-7 tools_4.2.2
[10] zlibbioc_1.44.0 lifecycle_1.0.3 tibble_3.2.1
[13] lattice_0.20-45 pkgconfig_2.0.3 rlang_1.1.1
[16] Matrix_1.5-1 DelayedArray_0.24.0 cli_3.6.1
[19] rstudioapi_0.15.0 GenomeInfoDbData_1.2.9 dplyr_1.1.2
[22] generics_0.1.3 S4Vectors_0.36.2 vctrs_0.6.3
[25] IRanges_2.32.0 stats4_4.2.2 grid_4.2.2
[28] tidyselect_1.2.0 glue_1.6.2 Biobase_2.58.0
[31] R6_2.5.1 fansi_1.0.4 RProtoBufLib_2.10.0
[34] magrittr_2.0.3 matrixStats_1.0.0 BiocGenerics_0.44.0
[37] GenomicRanges_1.50.2 SummarizedExperiment_1.28.0 flowCore_2.10.0
[40] utf8_1.2.3 RCurl_1.98-1.12 rjson_0.2.21

JManickam13 commented 1 year ago

*apologies if there is not enough information. This is my first time posting a problem

thomasyu888 commented 1 year ago

Thanks for reporting this issue @JManickam13 .

At first glance, it appears that your system uses python 3.11 which is incompatible with the pandas version that this package requires.

I am working on a client release soon which should hopefully resolve this issue. Let me dig into your error message more in case I am incorrect.

JManickam13 commented 1 year ago

In this case, should I download an older version of python? would that make the installation work?

thomasyu888 commented 1 year ago

Yes, that should work. Sorry for the trouble!