kimyen
commented
5 years ago Hello @xtYao , thank you for reporting the issue. synapser package uses a separate Python environment. This environment is separated from the user's Python environment. We designed the package this way, so that installation of synapser won't affect the user's Python environment and when user changes their Python environment, it won't affect the package.
For synapser to successfully install it dependencies including Python, please verify that your machine has all the required dependencies. Please see this articles for the required dependencies: https://r-docs.synapse.org/articles/systemDependencies.html. Your output seems like you should have the required dependencies to get this far. However, I would like to double check this case, making sure we do not miss a step here. Please let me know if you had the required dependencies, and the problem persist. Thank you.
Operating system
CentOS 7
Description of the problem
python urllib3 module not found during synapser installation even though the package is already there.
Expected behavior
Python should be able to find urllib3 as I saw from running this line in a python console:
bash:mskilab01:~/software 1002 $ python
Python 3.5.2 (default, Oct 27 2016, 10:30:44)
[GCC 4.9.2 20150212 (Red Hat 4.9.2-6)] on linux
Type "help", "copyright", "credits" or "license" for more information.
Actual behavior
File Edit Options Buffers Tools iESS Complete In/Out Signals Help
Using /gpfs/commons/home/xyao/.local/lib/python3.5/site-packages
Searching for urllib3==1.23
Best match: urllib3 1.23
Adding urllib3 1.23 to easy-install.pth file
Using /gpfs/commons/home/xyao/.local/lib/python3.5/site-packages
Searching for idna==2.7
Best match: idna 2.7
Adding idna 2.7 to easy-install.pth file
Using /gpfs/commons/home/xyao/.local/lib/python3.5/site-packages
Searching for chardet==3.0.4
Best match: chardet 3.0.4
Adding chardet 3.0.4 to easy-install.pth file
Installing chardetect script to /tmp/RtmpeV96TB/R.INSTALLc00a729021d7/synapser/inst/bin
Using /gpfs/commons/home/xyao/.local/lib/python3.5/site-packages
Finished processing dependencies for synapseclient==1.9.2
Traceback (most recent call last):
File "", line 1, in
File "/tmp/RtmpeV96TB/R.INSTALLc00a729021d7/synapser/inst/python/installPythonClient.py", line 82, in main
import synapseclient
File "/tmp/RtmpeV96TB/R.INSTALLc00a729021d7/synapser/inst/lib/python3.5/site-packages/synapseclient-1.9.2-py3.5.egg/s\ ynapseclient/init.py", line 274, in
from .client import Synapse, login
File "/tmp/RtmpeV96TB/R.INSTALLc00a729021d7/synapser/inst/lib/python3.5/site-packages/synapseclient-1.9.2-py3.5.egg/s\ ynapseclient/client.py", line 78, in
from . import cache
File "/tmp/RtmpeV96TB/R.INSTALLc00a729021d7/synapser/inst/lib/python3.5/site-packages/synapseclient-1.9.2-py3.5.egg/s\ ynapseclient/cache.py", line 26, in
from synapseclient.lock import Lock
File "/tmp/RtmpeV96TB/R.INSTALLc00a729021d7/synapser/inst/lib/python3.5/site-packages/synapseclient-1.9.2-py3.5.egg/s\ ynapseclient/lock.py", line 12, in
from synapseclient.exceptions import *
File "/tmp/RtmpeV96TB/R.INSTALLc00a729021d7/synapser/inst/lib/python3.5/site-packages/synapseclient-1.9.2-py3.5.egg/s\ ynapseclient/exceptions.py", line 20, in
import requests
File "/tmp/RtmpeV96TB/R.INSTALLc00a729021d7/synapser/inst/lib/python3.5/site-packages/requests-2.22.0-py3.5.egg/reque\ sts/init.py", line 43, in
import urllib3
ImportError
:
No module named 'urllib3'
Error in PythonEmbedInR::pyExec(command) :
An error has occurred while executing Python code. See traceback above.
Execution halted
ERROR: configuration failed for package ‘synapser’
Output of
sessionInfo()Matrix products: default
BLAS: /nfs/sw/R/R-3.5.1/lib64/R/lib/libRblas.so
LAPACK: /nfs/sw/R/R-3.5.1/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Flow_0.0.0.9000 gGnome_0.1
[3] gTrack_0.1.0 Matrix_1.2-17
[5] skitools_0.0.0.9000 igraph_1.2.4
[7] reshape2_1.4.3 plotly_4.8.0
[9] ggplot2_3.1.1 stringr_1.4.0
[11] gUtils_0.2.0 data.table_1.12.2
[13] usethis_1.5.0 devtools_2.0.1
[15] htmlwidgets_1.3 VariantAnnotation_1.28.13
[17] Rsamtools_1.34.1 Biostrings_2.50.2
[19] XVector_0.22.0 SummarizedExperiment_1.12.0
[21] DelayedArray_0.8.0 BiocParallel_1.16.6
[23] matrixStats_0.54.0 Biobase_2.42.0
[25] GenomicRanges_1.34.0 GenomeInfoDb_1.18.2
[27] IRanges_2.16.0 S4Vectors_0.20.1
[29] BiocGenerics_0.28.0
loaded via a namespace (and not attached):
[1] bitops_1.0-6 fs_1.2.7 bit64_0.9-7
[4] progress_1.2.0 httr_1.4.0 rprojroot_1.3-2
[7] tools_3.5.1 backports_1.1.3 R6_2.4.0
[10] DBI_1.0.0 lazyeval_0.2.2 colorspace_1.4-1
[13] withr_2.1.2 tidyselect_0.2.5 prettyunits_1.0.2
[16] processx_3.3.0 bit_1.1-14 compiler_3.5.1
[19] cli_1.1.0 desc_1.2.0 rtracklayer_1.42.2
[22] scales_1.0.0 callr_3.2.0 digest_0.6.18
[25] pkgconfig_2.0.2 htmltools_0.3.6 sessioninfo_1.1.1
[28] BSgenome_1.50.0 rlang_0.3.4 RSQLite_2.1.1
[31] jsonlite_1.6 dplyr_0.8.0.1 RCurl_1.95-4.12
[34] magrittr_1.5 GenomeInfoDbData_1.2.0 Rcpp_1.0.1
[37] munsell_0.5.0 stringi_1.4.3 zlibbioc_1.28.0
[40] pkgbuild_1.0.3 plyr_1.8.4 grid_3.5.1
[43] blob_1.1.1 crayon_1.3.4 lattice_0.20-35
[46] GenomicFeatures_1.34.7 hms_0.4.2 ps_1.3.0
[49] pillar_1.3.1 biomaRt_2.38.0 pkgload_1.0.2
[52] XML_3.98-1.19 glue_1.3.1 remotes_2.0.2
[55] testthat_2.0.1 gtable_0.3.0 purrr_0.3.2
[58] tidyr_0.8.3 assertthat_0.2.1 viridisLite_0.3.0
[61] tibble_2.1.1 GenomicAlignments_1.18.1 AnnotationDbi_1.44.0
[64] memoise_1.1.0