CoGAPS checkpoints not enabled

[badoi]

I'm using scCoGAPS and haven't been able to use the checkpoint saving steps. I found that the checkpointsEnabled() is set to FALSE, with no clear way to change this. I've used the BiocManager to install CoGAPS as well as the conda bioconductor to install CoGAPS on a slurm unix cluster. I've also installed on a mac, and all forms didn't have checkpointsEnabled(). Any thoughts to turn on checkpoints will be much appreciated.

The compile settings (representative of one of these installations) is below.

SIMD: AVX instructions enabled
Compiler did not support OpenMP

R version 3.6.3 (2020-02-29)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /home/bnphan/miniconda3/envs/single-cell/lib/libopenblasp-r0.3.7.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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] CoGAPS_3.6.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6                cluster_2.1.0              
 [3] XVector_0.26.0              GenomicRanges_1.38.0       
 [5] BiocGenerics_0.32.0         zlibbioc_1.32.0            
 [7] IRanges_2.20.1              BiocParallel_1.20.1        
 [9] lattice_0.20-41             GenomeInfoDb_1.22.0        
[11] caTools_1.18.0              tools_3.6.3                
[13] SummarizedExperiment_1.16.0 parallel_3.6.3             
[15] grid_3.6.3                  rhdf5_2.30.1               
[17] Biobase_2.46.0              KernSmooth_2.23-16         
[19] gtools_3.8.2                matrixStats_0.56.0         
[21] Matrix_1.2-18               GenomeInfoDbData_1.2.2     
[23] Rhdf5lib_1.8.0              RColorBrewer_1.1-2         
[25] S4Vectors_0.24.4            bitops_1.0-6               
[27] SingleCellExperiment_1.8.0  RCurl_1.98-1.1             
[29] gdata_2.18.0                DelayedArray_0.12.0        
[31] compiler_3.6.3              gplots_3.0.3               
[33] stats4_3.6.3               ```

[badoi]

accidentally closed. Leaving open for when checkpoints is re-enabled on devel branch. Thanks for looking into this issue!

[ejfertig]

No problem. We are checking.

Sent from my iPhone

On Apr 17, 2020, at 10:17 AM, BaDoi Phan notifications@github.com wrote:



accidentally closed. Leaving open for when checkpoints is re-enabled on devel branch. Thanks for looking into this issue!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/FertigLab/CoGAPS/issues/49#issuecomment-615269490, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AATMMKZAP2TEFSORNS5RTGLRNBQFXANCNFSM4MIZUENQ.

WARNING: E-mail sent over the Internet is not secure. Information sent by e-mail may not remain confidential. DISCLAIMER: This e-mail is intended only for the individual to whom it is addressed. It may be used only in accordance with applicable laws. If you received this e-mail by mistake, notify the sender and destroy the e-mail.

[chlee-tabin]

I am also having the same issue. Is this issue fixed in develop version?

[MarcElosua]

Hi @FertigLab, thanks for such a great package! I am also having this issue, I'm running CoGAPS v3.14.0. How can I enable checkpoints? Thanks!

[ejfertig]

Thanks! It was disabled in our R interface, but we are looking into adding it back in. Please stay tuned.

Elana J. Fertig, PhD Director of the Quantitative Sciences Division co-Director Convergence Institute co-Director Single-Cell Consortium Associate Cancer Center Director of Quantitative Sciences Daniel Nathans Scientific Innovator Associate Professor of Oncology, Biomedical Engineering, and Applied Mathematics and Statistics Johns Hopkins University https://fertiglab.com @FertigLab

On Mar 15, 2022, at 5:39 PM, Marc Elosua Bayés @.**@.>> wrote:

Hi @FertigLabhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FFertigLab&data=04%7C01%7Cejfertig%40jhmi.edu%7Ceedca855d5e44111249508da06cc4a76%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637829771747522203%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=ALyMpnyENZlFfFHqR%2FHTzjL5e2tEvX0DGOIaajgaxfs%3D&reserved=0, thanks for such a great package! I am also having this issue, I'm running CoGAPS v3.14.0. How can I enable checkpoints? Thanks!

— Reply to this email directly, view it on GitHubhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FFertigLab%2FCoGAPS%2Fissues%2F49%23issuecomment-1068498036&data=04%7C01%7Cejfertig%40jhmi.edu%7Ceedca855d5e44111249508da06cc4a76%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637829771747522203%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=H289lMawpd22liM2oBN8nWSIOJshE2Douzv%2BRVVrwwk%3D&reserved=0, or unsubscribehttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAATMMK2KJEZWB3SSS4QHGDLVAD7RFANCNFSM4MIZUENQ&data=04%7C01%7Cejfertig%40jhmi.edu%7Ceedca855d5e44111249508da06cc4a76%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637829771747522203%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=G%2BDWGS6D%2BwcpPvcIKZfupyOLY0YLNaCkoEsohYtWEPA%3D&reserved=0. You are receiving this because you commented.Message ID: @.***>