Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:08:36 -0400 (Fri, 18 Mar 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
To the developers/maintainers of the scAlign package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scAlign.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1710/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scAlign 1.9.0 (landing page) Nelson Johansen
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
riesling1 | Windows Server 2019 Standard / x64 | OK | OK | ERROR | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
Package: scAlign |
Version: 1.9.0 |
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scAlign.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings scAlign_1.9.0.tar.gz |
StartedAt: 2022-03-17 20:10:57 -0400 (Thu, 17 Mar 2022) |
EndedAt: 2022-03-17 20:14:05 -0400 (Thu, 17 Mar 2022) |
EllapsedTime: 188.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: scAlign.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scAlign.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings scAlign_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/scAlign.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'scAlign/DESCRIPTION' ... OK * this is package 'scAlign' version '1.9.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'SingleCellExperiment', 'Seurat', 'tensorflow', 'purrr', 'irlba', 'Rtsne', 'ggplot2', 'FNN' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'scAlign' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .check_all_args: no visible global function definition for 'metadata' .check_all_args: no visible global function definition for 'assays' .data_setup: no visible global function definition for 'assays' .data_setup: no visible global function definition for 'assay' PlotTSNE: no visible global function definition for 'assays' PlotTSNE: no visible binding for global variable 'scAlignHSC' PlotTSNE: no visible global function definition for 'assay' scAlign: no visible global function definition for 'metadata' scAlign: no visible global function definition for 'metadata<-' scAlignCreateObject: no visible global function definition for 'colData<-' scAlignCreateObject: no visible global function definition for 'metadata' scAlignCreateObject: no visible global function definition for 'metadata<-' scAlignCreateObject: no visible global function definition for 'assays' scAlignCreateObject: no visible global function definition for 'assay' scAlignCreateObject: no visible global function definition for 'GetCellEmbeddings' scAlignCreateObject: no visible global function definition for 'GetGeneLoadings' scAlignCreateObject : <anonymous>: no visible global function definition for 'assay' scAlignMulti: no visible global function definition for 'metadata' scAlignMulti: no visible global function definition for 'metadata<-' scAlignMulti: no visible global function definition for 'assays' scAlignMulti: no visible global function definition for 'assay' Undefined global functions or variables: GetCellEmbeddings GetGeneLoadings assay assays colData<- metadata metadata<- scAlignHSC * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... WARNING Files not of a type allowed in a 'data' directory: 'DESCRIPTION' 'LICENSE' 'NAMESPACE' 'NEWS' 'README.md' Please use e.g. 'inst/extdata' for non-R data files * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'scAlign-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: gaussianKernel > ### Title: Computes gaussian kernel matrix > ### Aliases: gaussianKernel > > ### ** Examples > > > ## Input data, 100 cells x 10 features > data = matrix(sample.int(1000, 100*10, TRUE), 100, 10) > rownames(data) = paste0("cell", seq_len(100)) > colnames(data) = paste0("gene", seq_len(10)) > > result = gaussianKernel(data, nrow(data)) Error in py_call_impl(callable, dots$args, dots$keywords) : ValueError: Tried to convert 'shape' to a tensor and failed. Error: Cannot convert a partially known TensorShape to a Tensor: (None, 1) Detailed traceback: File "C:\Python38\lib\site-packages\tensorflow\python\util\dispatch.py", line 201, in wrapper return target(*args, **kwargs) File "C:\Python38\lib\site-packages\tensorflow\python\ops\array_ops.py", line 195, in reshape result = gen_array_ops.reshape(tensor, shape, name) File "C:\Python38\lib\site-packages\tensorflow\python\ops\gen_array_ops.py", line 8233, in reshape _, _, _op, _outputs = _op_def_library._apply_op_helper( File "C:\Python38\lib\site-packages\tensorflow\python\framework\op_def_library.py", line 486, in _apply_op_helper raise ValueError( Calls: gaussianKernel ... tryCatchList -> force -> <Anonymous> -> py_call_impl Execution halted * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 3 NOTEs See 'D:/biocbuild/bbs-3.15-bioc/meat/scAlign.Rcheck/00check.log' for details.
scAlign.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL scAlign ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'scAlign' ... ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'scAlign' finding HTML links ... done GetCrit html PlotTSNE html RunMultiCCA html UpdateW html alignment_score html cellbench html compute_kernel_matrix html decoderModel_add_mse_loss html decoderModel_calc_projection html decoderModel_create_train_op html decoderModel_emb_to_proj html decoderModel_train_decoder html decoder_large html decoder_medium html decoder_small html define_kernel_matrix html dot-check_all_args html dot-check_tensorflow html dot-data_setup html dot-early_stop html dot-is.wholenumber html dot-learning_rate html dot-plotTSNE html encoderModel_add_logit_loss html encoderModel_add_semisup_loss_data_driven html encoderModel_calc_embedding html encoderModel_calc_logit html encoderModel_create_train_op html encoderModel_data_to_embedding html encoderModel_embedding_to_logit html encoderModel_gaussian_kernel html encoderModel_train_encoder html encoderModel_train_encoder_multi html encoder_large html encoder_medium html encoder_small html gaussianKernel html l2n html scAlign html scAlignArguments html scAlignCreateObject html scAlignMulti html scAlignOptions html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scAlign) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'singscore' is missing or broken done
scAlign.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > > test_check("scAlign") Loading required package: scAlign Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Loading required package: Seurat Attaching SeuratObject Attaching package: 'Seurat' The following object is masked from 'package:SummarizedExperiment': Assays Loading required package: tensorflow Loading required package: purrr Attaching package: 'purrr' The following object is masked from 'package:GenomicRanges': reduce The following object is masked from 'package:IRanges': reduce The following object is masked from 'package:testthat': is_null Loading required package: irlba Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand Loading required package: Rtsne Loading required package: ggplot2 Loading required package: FNN 2022-03-17 20:13:54.305069: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'cudart64_101.dll'; dlerror: cudart64_101.dll not found 2022-03-17 20:13:54.305371: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. 2022-03-17 20:13:56.303138: W tensorflow/stream_executor/platform/default/dso_loader.cc:59] Could not load dynamic library 'nvcuda.dll'; dlerror: nvcuda.dll not found 2022-03-17 20:13:56.303602: W tensorflow/stream_executor/cuda/cuda_driver.cc:312] failed call to cuInit: UNKNOWN ERROR (303) 2022-03-17 20:13:56.306782: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:169] retrieving CUDA diagnostic information for host: riesling1 2022-03-17 20:13:56.307088: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:176] hostname: riesling1 2022-03-17 20:13:56.307873: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN)to use the following CPU instructions in performance-critical operations: AVX2 To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. 2022-03-17 20:13:56.325451: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x7e29a840 initialized for platform Host (this does not guarantee that XLA will be used). Devices: 2022-03-17 20:13:56.325783: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version TensorFlow check: [Passed] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ] > > proc.time() user system elapsed 9.10 1.42 10.86
scAlign.Rcheck/scAlign-Ex.timings
name | user | system | elapsed | |
PlotTSNE | 3.61 | 0.95 | 4.82 | |