• using R Under development (unstable) (2024-12-13 r87441)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 19.1.5     flang-new version 19.1.5
• running under: Fedora Linux 36 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘simule/DESCRIPTION’ ... OK
• this is package ‘simule’ version ‘1.3.0’
• 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 executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘simule’ can be installed ... [5s/10s] OK See the install log for details.
• checking installed package size ... OK
• checking package 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 loading without being on the library search path ... OK
• checking use of S3 registration ... 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 ... [9s/12s] OK
• checking Rd files ... NOTE checkRd: (-1) simule-package.Rd:18: Lost braces; missing escapes or markup?     18 | Identifying context-specific entity networks from aggregated data is an important task, often arising in bioinformatics and neuroimaging. Computationally, this task can be formulated as jointly estimating multiple different, but related, sparse Undirected Graphical Models (UGM) from aggregated samples across several contexts. Previous joint-UGM studies have mostly focused on sparse Gaussian Graphical Models (sGGMs) and can't identify context-specific edge patterns directly. We, therefore, propose a novel approach, SIMULE (detecting Shared and Individual parts of MULtiple graphs Explicitly) to learn multi-UGM via a constrained L1 minimization. SIMULE automatically infers both specific edge patterns that are unique to each context and shared interactions preserved among all the contexts. Through the L1 constrained formulation, this problem is cast as multiple independent subtasks of linear programming that can be solved efficiently in parallel. In addition to Gaussian data, SIMULE can also handle multivariate nonparanormal data that greatly relaxes the normality assumption that many real-world applications do not follow. We provide a novel theoretical proof showing that SIMULE achieves a consistent result at the rate O(log(Kp)/n_{tot}). On multiple synthetic datasets and two biomedical datasets, SIMULE shows significant improvement over state-of-the-art multi-sGGM and single-UGM baselines.        | ^ checkRd: (-1) simule.Rd:18: Lost braces     18 | level of the matrices. The \\eqn{\\lambda_n} in the following section:        | ^ checkRd: (-1) simule.Rd:23: Lost braces     23 | of each graph. The \\eqn{\\epsilon} in the following section: Details. If        | ^ checkRd: (-1) simule.Rd:62-65: Lost braces     62 | following equation: \\deqn{ \\hat{\\Omega}^{(1)}_I, \\hat{\\Omega}^{(2)}_I,        | ^ checkRd: (-1) simule.Rd:62: Lost braces     62 | following equation: \\deqn{ \\hat{\\Omega}^{(1)}_I, \\hat{\\Omega}^{(2)}_I,        | ^ checkRd: (-1) simule.Rd:62: Lost braces; missing escapes or markup?     62 | following equation: \\deqn{ \\hat{\\Omega}^{(1)}_I, \\hat{\\Omega}^{(2)}_I,        | ^ checkRd: (-1) simule.Rd:62: Lost braces     62 | following equation: \\deqn{ \\hat{\\Omega}^{(1)}_I, \\hat{\\Omega}^{(2)}_I,        | ^ checkRd: (-1) simule.Rd:62: Lost braces; missing escapes or markup?     62 | following equation: \\deqn{ \\hat{\\Omega}^{(1)}_I, \\hat{\\Omega}^{(2)}_I,        | ^ checkRd: (-1) simule.Rd:63: Lost braces     63 | \\dots, \\hat{\\Omega}^{(K)}_I, \\hat{\\Omega}_S =        | ^ checkRd: (-1) simule.Rd:63: Lost braces; missing escapes or markup?     63 | \\dots, \\hat{\\Omega}^{(K)}_I, \\hat{\\Omega}_S =        | ^ checkRd: (-1) simule.Rd:63: Lost braces     63 | \\dots, \\hat{\\Omega}^{(K)}_I, \\hat{\\Omega}_S =        | ^ checkRd: (-1) simule.Rd:64: Lost braces     64 | \\min\\limits_{\\Omega^{(i)}_I,\\Omega_S}\\sum\\limits_i ||\\Omega^{(i)}_I||_1+        | ^ checkRd: (-1) simule.Rd:64: Lost braces; missing escapes or markup?     64 | \\min\\limits_{\\Omega^{(i)}_I,\\Omega_S}\\sum\\limits_i ||\\Omega^{(i)}_I||_1+        | ^ checkRd: (-1) simule.Rd:64: Lost braces; missing escapes or markup?     64 | \\min\\limits_{\\Omega^{(i)}_I,\\Omega_S}\\sum\\limits_i ||\\Omega^{(i)}_I||_1+        | ^ checkRd: (-1) simule.Rd:65-67: Lost braces     65 | \\epsilon K||\\Omega_S||_1 } Subject to : \\deqn{        | ^ checkRd: (-1) simule.Rd:66: Lost braces; missing escapes or markup?     66 | ||\\Sigma^{(i)}(\\Omega^{(i)}_I + \\Omega_S) - I||_{\\infty} \\le \\lambda_{n}, i        | ^ checkRd: (-1) simule.Rd:66: Lost braces; missing escapes or markup?     66 | ||\\Sigma^{(i)}(\\Omega^{(i)}_I + \\Omega_S) - I||_{\\infty} \\le \\lambda_{n}, i        | ^ checkRd: (-1) simule.Rd:66: Lost braces; missing escapes or markup?     66 | ||\\Sigma^{(i)}(\\Omega^{(i)}_I + \\Omega_S) - I||_{\\infty} \\le \\lambda_{n}, i        | ^ checkRd: (-1) simule.Rd:66: Lost braces; missing escapes or markup?     66 | ||\\Sigma^{(i)}(\\Omega^{(i)}_I + \\Omega_S) - I||_{\\infty} \\le \\lambda_{n}, i        | ^ checkRd: (-1) simule.Rd:68: Lost braces     68 | \\eqn{\\lambda_n} is the hyperparameter controlling the sparsity level of the        | ^ checkRd: (-1) simule.Rd:69: Lost braces     69 | matrices and it is the \\code{lambda} in our function. The \\eqn{\\epsilon} is        | ^ checkRd: (-1) simule.Rd:69: Lost braces     69 | matrices and it is the \\code{lambda} in our function. The \\eqn{\\epsilon} is        | ^ checkRd: (-1) simule.Rd:72: Lost braces     72 | \\code{epsilon} parameter in our function and the default value is 1. For        | ^ checkRd: (-1) simule.Rd:47: Lost braces     47 | \\item{Graphs}{A list of the estimated inverse        | ^ checkRd: (-1) simule.Rd:47-48: Lost braces     47 | \\item{Graphs}{A list of the estimated inverse        | ^ checkRd: (-1) simule.Rd:48: Lost braces     48 | covariance/correlation matrices.} \\item{share}{The share graph among        | ^ checkRd: (-1) simule.Rd:48-49: Lost braces     48 | covariance/correlation matrices.} \\item{share}{The share graph among        | ^
• checking Rd metadata ... OK
• checking Rd line widths ... 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 ... OK
• checking data for non-ASCII characters ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... OK
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 NOTE