Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 |
Package 444/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
COSNet 1.40.0 (landing page) Marco Frasca
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the COSNet package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COSNet.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: COSNet |
Version: 1.40.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COSNet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COSNet_1.40.0.tar.gz |
StartedAt: 2024-12-20 15:47:49 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 15:48:29 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 39.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: COSNet.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COSNet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COSNet_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/COSNet.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘COSNet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘COSNet’ version ‘1.40.0’ * checking package namespace information ... OK * checking package dependencies ... OK * 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 for sufficient/correct file permissions ... OK * checking whether package ‘COSNet’ can be installed ... OK * used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 whether startup messages can be suppressed ... NOTE COSNet: Cost-Sensitive algorithm for binary classification in graphs. It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * 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 File ‘COSNet/R/COSNet.R’: .onAttach calls: cat("COSNet: Cost-Sensitive algorithm for binary classification in graphs.\n") Package startup functions should use ‘packageStartupMessage’ to generate messages. See section ‘Good practice’ in '?.onAttach'. generate_labels: no visible global function definition for ‘runif’ Undefined global functions or variables: runif Consider adding importFrom("stats", "runif") to your NAMESPACE file. * checking Rd files ... WARNING checkRd: (7) COSNet-package.Rd:30: Invalid email address: {frasca,valentini}@di.unimi.it checkRd: (-1) COSNet.Rd:32: Lost braces; missing escapes or markup? 32 | {1) Generating a random labeling (1, -1) for unlabeled nodes. } | ^ checkRd: (-1) COSNet.Rd:33: Lost braces; missing escapes or markup? 33 | {2) Learning the parameters "alpha and "c" such that the line "cos(alpha)*y - sin(alpha)*x - q*cos(alpha) = 0 " linearly separates a suitable set of labeled points (in which each point corresponds to a labeled node) and optimizes (in terms of alpha and q) the F-score criterion. The output of this phase is the intercept "q" of the optimum line and the corresponding angle "alpha". Then each neuron has threshold c = - q*cos(alpha).} | ^ checkRd: (-1) COSNet.Rd:34: Lost braces; missing escapes or markup? 34 | {3) Extending "c" and "alpha" to the subnetwork composed of only unlabeled nodes, and simulating it until an equilibrium state is reached. The dynamics of this network is regularized by adding a term to the energy function that is minimized when the proportion of positive in the network state is roughly the proportion of positives in the labeled part of the network. The parameter "cost" corresponds to the parameter beta in the equation eta = beta*|tan((alpha - pi/4)*2)| (see Frasca et al. 2013). When the equilibrium state is reached, positive nodes will be predicted as positive for the current task.} | ^ checkRd: (-1) generate_labels.Rd:26: Lost braces; missing escapes or markup? 26 | This function generates "n" random labels in {-1, 1} drawn from the binomial distribution B(n, pos_rate) | ^ checkRd: (-1) runSubnet.Rd:38: Lost braces; missing escapes or markup? 38 | Function to simulate the subnetwork composed of the unlabeled genes, in which each neuron has {sin(alpha_value), -cos(alpha_value)} as activation value, and | ^ * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/COSNet/libs/COSNet.so’: Found ‘_rand’, possibly from ‘rand’ (C) Found ‘_srand’, possibly from ‘srand’ (C) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed cosnet.cross.validation 11.871 1.923 13.83 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/COSNet.Rcheck/00check.log’ for details.
COSNet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL COSNet ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘COSNet’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c COSNet.c -o COSNet.o COSNet.c:403:61: warning: variable 'tn_o' set but not used [-Wunused-but-set-variable] int N_pos = 0, pos_halfplane = 0, N_neg, tp_o, fn_o, fp_o, tn_o, tp_u, fn_u, fp_u, tn_u, ^ 1 warning generated. clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o COSNet.so COSNet.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-COSNet/00new/COSNet/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location COSNet: Cost-Sensitive algorithm for binary classification in graphs. ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location COSNet: Cost-Sensitive algorithm for binary classification in graphs. ** testing if installed package keeps a record of temporary installation path * DONE (COSNet)
COSNet.Rcheck/tests/runTests.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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. > BiocGenerics:::testPackage("COSNet") COSNet: Cost-Sensitive algorithm for binary classification in graphs. 0.468 RUNIT TEST PROTOCOL -- Fri Dec 20 15:48:19 2024 *********************************************** Number of test functions: 9 Number of errors: 0 Number of failures: 0 1 Test Suite : COSNet RUnit Tests - 9 test functions, 0 errors, 0 failures Number of test functions: 9 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 0.477 0.077 0.541
COSNet.Rcheck/COSNet-Ex.timings
name | user | system | elapsed | |
COSNet | 0.560 | 0.034 | 0.597 | |
cosnet.cross.validation | 11.871 | 1.923 | 13.830 | |
find.division.not.strat | 0.001 | 0.000 | 0.001 | |
find.division.strat | 0.001 | 0.000 | 0.001 | |
generate_labels | 0 | 0 | 0 | |
generate_points | 0.001 | 0.000 | 0.002 | |
optimize_pos_above | 0.367 | 0.036 | 0.402 | |
optimizep | 0.316 | 0.027 | 0.343 | |
reg_data | 0.497 | 0.058 | 0.555 | |
runSubnet | 0.409 | 0.056 | 0.465 | |